Why does DataStore only save the Stats and not the BoolValues?

Unfortunately, your question was a bit more complex than I though it was, but I am sure I can still answer it.
Step 1. You want to create a folder of bool values in the player, each one named for ex: HasM9, HasM82 etc, each one should be false.
Then you want to create your data-store, I haven't changed mine to fit your question, but I have added lots of comments so you know what to do with the code.
Note : You should save tables on your keys, not individual values, each key can take alot, and it will lower how many times you access the data-store, lowering the chance of the data store budget being reached. Make sure to also use one datastore, not lots of datastores, unless each datastore holds different types of data, e.g XP datastore, Gun datastore etc. Your datastore should have a Unique name, this prevents the data you have saved being overwritten by data that has been saved in other games, also make sure your keys have unique names, and use Player.UserId, because if a player changes their name, they lose all of their data.
A Module script, in ServerScriptService

local module = {}
local DataStoreService = game:GetService("DataStoreService") --get DataStoreService
local InventoryItems = DataStoreService:GetDataStore("InventoryItems") --Change it to whatever you want to call it e.g :GetDataStore("examplename"), should be complex name
AUTOSAVE_INTERVAL = 120 --should be no lower than 60 (DataStore Budget)

game.Players.PlayerAdded:Connect(function(Player) --When a player is added to the game, load in their data
    local Key = 'PlayerIdNum-'..Player.UserId.."_InvItemKey" --"This is the key you use to save players data on (must be no longer than 50 characters and must be unique)
    --The key is also what you use to load data as well so it MUST be the exact same variable in the other parts of the script
    --Values to Save (create them also, e.g instance.new)
    local InvData = Player:WaitForChild("Backpack"):WaitForChild("Inventory") --The folder of values you want to save
    local Bananas = InvData:WaitForChild("Bananas")
    local Apples = InvData:WaitForChild("Apples")
    local FirstAid = InvData:WaitForChild("FirstAid")
    local Coconuts = InvData:WaitForChild("Coconuts")
    local MetalScraps = InvData:WaitForChild("MetalScraps")
    local Logs = InvData:WaitForChild("Logs")
    local Sticks = InvData:WaitForChild("Sticks")


    --DataStore Stuff
    --The table that is used to save it after it is all loaded in
    local StoreToSet = {}
    --Get the data and store it
    local DataToGet = InventoryItems:GetAsync(Key) --Returns the data the key stores (as a table)
    --Changing the table back into values
    if DataToGet ~= nil then --If there is a table
        if #DataToGet >= 1 then --If the table length is 1 or more
            print("Has Data")
            --For each value you have, copy the below code (MUST BE IN ORDER OF SAVED IN!)
            if DataToGet[1] ~= nil then --if the first bit of data in the table does exist
                Bananas.Value = DataToGet[1] --Set the values of bananas as that value
                table.insert(StoreToSet , DataToGet[1]) --Store it in another table so it can be saved
            end
            if DataToGet[2] ~= nil then
                Apples.Value = DataToGet[2]
                table.insert(StoreToSet , DataToGet[2])
            end
            if DataToGet[3] ~= nil then
                FirstAid.Value = DataToGet[3]
                table.insert(StoreToSet , DataToGet[3])
            end
            if DataToGet[4] ~= nil then
                Coconuts.Value = DataToGet[4]
                table.insert(StoreToSet , DataToGet[4])
            end
            if DataToGet[5] ~= nil then
                MetalScraps.Value = DataToGet[5]
                table.insert(StoreToSet , DataToGet[5])
            end
            if DataToGet[6] ~= nil then
                Logs.Value = DataToGet[6]
                table.insert(StoreToSet , DataToGet[6])
            end
            if DataToGet[7] ~= nil then
                Sticks.Value = DataToGet[7]
                table.insert(StoreToSet , DataToGet[7])
            end
        print(DataToGet[1], DataToGet[2], DataToGet[3], DataToGet[4], DataToGet[5], DataToGet[6], DataToGet[7] .. " Data") --Print the data values
        end
    else
        DataToGet = {} --Create a table, since there was no data or table returned in the GetAsync (this only happens with new players)
        DataToGet[1] = Bananas.Value --The first bit of data in the table is equal to Bananas.Value
        Bananas.Value = 0 --Make sure it is 0
        table.insert(StoreToSet , DataToGet[1]) --Insert it into table, so it can be saved, so next time they join, it loads a table
        DataToGet[2] = Apples.Value
        Apples.Value = 0
        table.insert(StoreToSet , DataToGet[2])
        DataToGet[3] = FirstAid.Value
        FirstAid.Value = 0
        table.insert(StoreToSet , DataToGet[3])
        DataToGet[4] = Coconuts.Value
        Coconuts.Value = 0
        table.insert(StoreToSet , DataToGet[4])
        DataToGet[5] = MetalScraps.Value
        MetalScraps.Value = 0
        table.insert(StoreToSet , DataToGet[5])
        DataToGet[6] = Logs.Value
        Logs.Value = 0
        table.insert(StoreToSet , DataToGet[6])
        DataToGet[7] = Sticks.Value
        Sticks.Value = 0
        table.insert(StoreToSet , DataToGet[7])
        print(DataToGet[1], DataToGet[2], DataToGet[3], DataToGet[4], DataToGet[5], DataToGet[6], DataToGet[7] .. " New Data") --Print new data (all should be 0)
    end
    InventoryItems:SetAsync(Key, StoreToSet) --Set the data to the key as a table, so next time they join there is a table to load in (only affects the first time they join)
end)

game.Players.PlayerRemoving:Connect(function(Player) --When the player leaves the game, save their data
    local Key = 'PlayerIdNum-'..Player.UserId.."_InvItemKey" --"This is the key you use to save players data on (must be no longer than 50 characters and must be unique)
    --The key is also what you use to load data as well so it MUST be the exact same variable in the other parts of the script
    --Values to Save
    local InvData = Player:WaitForChild("Backpack"):WaitForChild("Inventory")
    local Bananas = InvData:WaitForChild("Bananas")
    local Apples = InvData:WaitForChild("Apples")
    local FirstAid = InvData:WaitForChild("FirstAid")
    local Coconuts = InvData:WaitForChild("Coconuts")
    local MetalScraps = InvData:WaitForChild("MetalScraps")
    local Logs = InvData:WaitForChild("Logs")
    local Sticks = InvData:WaitForChild("Sticks")
    --Put what you need to save here (THE ORDER YOU USE IN THIS IS THE ORDER YOU MUST USE WHEN THEY JOIN)
    local DataToSave = {
        Bananas.Value, --must put.Value after or it will error
        Apples.Value,
        FirstAid.Value,
        Coconuts.Value,
        MetalScraps.Value,
        Logs.Value,
        Sticks.Value,
    }
    InventoryItems:SetAsync(Key, DataToSave)
end)

--You may want to reorder this
--Autosaving
spawn(function()
    while wait(AUTOSAVE_INTERVAL) do
        for i, Player in pairs (game:GetService("Players"):GetChildren()) do --for every player in the game, save
            print("Auto-saving " .. Player.Name .. "'s Data")
            local Key = 'PlayerIdNum-'..Player.UserId.."_InvItemKey"
            local InvData = Player:WaitForChild("Backpack"):WaitForChild("Inventory")
            local Bananas = InvData:WaitForChild("Bananas")
            local Apples = InvData:WaitForChild("Apples")
            local FirstAid = InvData:WaitForChild("FirstAid")
            local Coconuts = InvData:WaitForChild("Coconuts")
            local MetalScraps = InvData:WaitForChild("MetalScraps")
            local Logs = InvData:WaitForChild("Logs")
            local Sticks = InvData:WaitForChild("Sticks")
            local DataToSave = {
                Bananas.Value,
                Apples.Value,
                FirstAid.Value,
                Coconuts.Value,
                MetalScraps.Value,
                Logs.Value,
                Sticks.Value,
            }
            InventoryItems:SetAsync(Key, DataToSave)
            print("Successfully Auto-saved " .. Player.Name .. "'s Data")
        end
    end
end)

return module

A normal script, but a child/decendent of/inside of the module script

require(script.Parent)

After this, you will want another script that reads the values and gives them the tools based on the bool value, e.g:(local)

local player = game.Players.LocalPlayer
if player.Folder.HasM9.Value == true then
    local m9 = game.replicatedstorage.M9:Clone()
    m9.Parent = player.Backpack
end

I hope you can edit the script I have provided, to help you with your problem, if it has helped, please remember to accept the answer! :)