debounce ruins my script ( Advance? )

Your best option is to move the code to a LocalScript so that it runs on the client, and can be coded just as you have done. The caveat here is that you can't just put a LocalScript into a Model or part in Workspace, the script has to reside in a place where LocalScripts can execute from or get clone to an executable place from (LocalScripts in StarterPlayerScripts, StarterGui, etc. get copied into each players' PlayerScripts or PlayerGui respectively), and it needs to get a reference to the part or model it's associate with via a WaitForChild() call.

To make your script work as a server Script, it needs to be multiplayer-aware, which means you can't have a single debounce boolean, you need one bool per player. Normally, this sort of thing would be done with a table, like so (note: untested edits to your code):

local Popup = script.Parent.Popup
local debounce = {}

function onTouch(hit)
    local humanoid = hit.Parent:FindFirstChildOfClass("Humanoid")
    local player = humanoid and game.Players:FindFirstChild(humanoid.Parent.Name)
    if player and (not debounce[player]) then
        debounce[player] = true
        local Gui = Popup:clone()
        Gui.Parent = player.PlayerGui

        Wait(4)
        Gui:Destroy()


        Wait(1)
        debounce[player] = nil
    end
end

script.Parent.Touched:connect(onTouch)

That said, the code should properly be moved to a LocalScript. Doing this sort of thing on the server means everyone sees the popup's appearance lag by the amount of their round-trip ping time + time to replicate the necessary Gui. Even when you have a touched event that changes server state, it can be beneficial to process it on the client and then send a RemoteEvent to the server if the server needs to also do something.

For first, :connect, :remove and :clone its deprecated, use: :Connect, :Destroy and :Clone, And i recommend to use local variables, not variable = ..., but use local variable = ...

Why this happens?

This happens because the debounce its for one player only, for make a debounce for every player you need a table to store character, player name or UserId. not a variable

Example:

local Debounces = {}

local function onTouch(Hit)
    if Hit.Parent:FindFirstChildOfClass("Humanoid") then --> Try to find a humanoid...
        local Player = game.Players:GetPlayerFromCharacter(Hit.Parent) --> Try to get the player
        if Player and not Debounces[Player.UserId] then --> This gets the player and check if Current Player Debounce is false or nil
            Debounces[Player.UserId] = true --> Set Current Player debounce to true
            print("Debounce")
            wait(4) --> After 4 seconds
            Debounces[Player.UserId] = false --> Set Current Player debounce to false
        end
    end
end

script.Parent.Touched:Connect(onTouch)

With that, every player that touches, has a local debounce...

For your script only need to adjust that..

Fixed Script

local Popup = script.Parent.Popup
local Debounces = {}

local function onTouch(Hit)
    if Hit.Parent:FindFirstChildOfClass("Humanoid") then
        local Player = game.Players:GetPlayerFromCharacter(Hit.Parent)
        if Player and not Debounces[Player.UserId] then
            Debounces[Player.UserId] = true
            local Gui = Popup:Clone()
            Gui.Parent = Player:WaitForChild("PlayerGui")
            wait(4)
            Gui:Destroy()
            wait(1)
            Debounces[Player.UserId] = false
        end
    end
end

script.Parent.Touched:Connect(onTouch)

Hope it helped! :)