How to make that Shop gui open/close button at the same button?

You could add an open variable to use the same button

-- Core UI localscript
local open = false

local availableTools = game.ReplicatedStorage:WaitForChild("GetTools"):InvokeServer()
local mainFrame = script.Parent:WaitForChild("MainFrame")
local safeArea = mainFrame:WaitForChild("SafeArea")
local itemInformation = safeArea:WaitForChild("ItemInformation")
local infoFrame = itemInformation.InfoFrame
local selectedItem = itemInformation.SelectedItem
local equippedItem = itemInformation.EquippedItem
local numberOfItems = #availableTools

local itemFrame = safeArea.ItemFrame
local shopButton = script.Parent:WaitForChild("ShopButton")
local buyButton = infoFrame.BuyButton
local equippedItemViewport = script.Parent:WaitForChild("EquippedItemViewport")
local itemViewport = itemInformation.ItemViewport

shopButton.MouseButton1Down:Connect(function()
if open == false then
    mainFrame.Visible = true
    open = true
else
    mainFrame.Visible = false
    open = false
end
mainFrame.Visible = not mainFrame.Visible

end)

local PADDING_X = 0.02
local DROPDOWN_Y = 0.2
local DROPDOWN_X = 0.25

local item1 = itemFrame:WaitForChild("Item1")

local box
local numRows = 1

for i = 1,numberOfItems,1 do

    if i == 1 then
        box = item1
    else

        box = item1:Clone()
        box.Name = "item"..i
        box.Parent = itemFrame

        if (i-1) / (4*numRows) == 1 then
            -- New Row
            numRows = numRows + 1
            box.Position = UDim2.new (PADDING_X,0,box.Position.Y.Scale,0) + UDim2.new(0,0,DROPDOWN_Y*(numRows - 1))
        else
            -- Add  TO THE X ONLY
            box.Position = itemFrame["item"..(i-1)]
        end
    end
end

There is a simple way of doing this.

for the on button click you can type this code:

shopButton.MouseButton1Down:Connect(function()
    mainFrame.Visible = not mainFrame.Visible;
end);

when putting not there, if visible is true then not means false, if visible is false then not means true. not can mean opposite or in stuff like if statements you can do "if not 1 > 2 then" as in if 1 is not greater than 2. I hope this explanation helps you learn and the code can be kept simple.