why doesnt the debounce affect this animation?

The method Play only plays the animation but also continues the code so you are resetting the denounce not waiting till the animation finishes.

local clicked = false
 local swingAnim  = nil -- store animation
tool.Activated:connect(function()

--check animation status
if swingAnim   ~= nil then
    clicked = swingAnim:IsPlaying () -- now check that the animation has finished
end

    if not clicked then
            clicked = true
            if swing1 and humanoid and humanoid.Health > 0 then
                local swingAnim = humanoid:LoadAnimation(swing1)
                swingAnim:Play()
            end
        -- clicked = false we now don't need this
    end
end)

Hope this helps comment if you need any more info