How Do I Properly Set Up An Ammo System in Roblox?

Before I get into this, make sure you learn how to tab your script properly. Makes reading it and fixing problems much easier. Also in order to make your script cleaner it's better not to connect two functions inside of each other like you did with the Tool.Equipped then the Mouse.ButtonClick

Instead Make a variable named Equipped and change it to true once and once you click if that variable is true the rest will fire. I've put it inside of the code for you.

Actual Problem So basically you put local ammo inside of tool.Equipped which makes the ammo 5 everytime you equip the weapon. So take the variable local ammo outside of the tool.Equipped function. and make it like so:

local tool = script.Parent
local player = game:GetService("Players").LocalPlayer
local gui = game.Players.LocalPlayer.PlayerGui.AmmoGui.AmmoBar
local Equipped = false
local ammo = 5 -- MAX AMMO IN CLIP Outside of the Tool.Equipped

tool.Equipped:Connect(function(mouse)
	Equipped = true
	gui.AmmoInClip.Text = ammo
end)
tool.Unequipped:Connect(function()
	Equipped = false
end)
	
mouse.Button1Down:connect(function()
        if ammo >= 1 and Equipped then -- if ammo is over or equal to 1, shoot, and if weapon is equipped
        print("Mouse pressed!")
        local ray = Ray.new(tool.Handle.CFrame.p, (mouse.Hit.p - tool.Handle.CFrame.p).unit * 300)
        local part, position = workspace:FindPartOnRay(ray, player.Character, false, true)
        local beam = Instance.new("Part", workspace)
        beam.BrickColor = BrickColor.new("Yellow")
        beam.FormFactor = "Custom"
        beam.Material = "Neon"
        beam.Transparency = 0.25
        beam.Anchored = true
        beam.Locked = true
        beam.CanCollide = false
        local distance = (tool.Handle.CFrame.p - position).magnitude
        beam.Size = Vector3.new(0.3, 0.3, distance)
        beam.CFrame = CFrame.new(tool.Handle.CFrame.p, position) * CFrame.new(0, 0, -distance / 2)

        game:GetService("Debris"):AddItem(beam, 0.01)
        if part then
            local humanoid = part.Parent:FindFirstChild("Humanoid")
            if not humanoid then
                humanoid = part.Parent.Parent:FindFirstChild("Humanoid")
            end
            if humanoid then
                humanoid:TakeDamage(30)
            end
            ammo = (ammo-1) -- Subtract - shot from ammo
            gui.AmmoInClip.Text = ammo
            end
        end
end)

If you want to learn how to save the actual ammo inside of it. Then all you would have to do is put NumberValue inside of the tool named: "Ammo" and use that instead of the variable named 'Ammo' that you have inside of the script. Decreasing this number value will keep it constant.

If you want to make something reload when you click it. You could add a click detector to like a brick(ammo pack) on the ground. Then inside of the brick make a script that says

script.Parent.ClickDetector.MouseClick:Connect(function(Player)
	if Player.Backpack:FindFirstChild(Tool.Name) then -- or wherever you put the tool
		Tool.Ammo = 5
	end
end)