Okay, I looked into it again, the problem is: there are twofull screen buttons, overlaping somewhat. One only centering the game, one achieving proper full screen.. When using one of them, the timer is not there, with the other one the timer is visible and functioning :)
I think this might be a UI scaling problem or something with how itch handles the web game. I have the feeling like ive seen this issue with other games as well, making some UI awkwardly placed. What I dont understand is why the key counter is visible even if they are also UI elements, so maybe you can see what the difference in their implementation is.
TLDR: There are two fullscreen buttons overlaping, one leading to your timer being invisible.