I wanted to use the 1 and 2 keys as increase and decrease brush size and the software didn't warn of any conflicts but it seems that they are already in use:
https://docs.krita.org/en/reference_manual/tools/zoom.html

Is there any way to remove this default shortcuts or change them? If not why would you let people use keys that are already in use without any warning seems counterproductive

Yes this is easy to miss, and I agree it should notice conflicts, but the "1" and "2" key bindings for zooming are found in "Canvas Input Settings" (the category below "Keyboard Shortcuts" in the Configure dialog), look at "Zoom Canvas" there, you can also change those (or set input to "None") and then bind those keys to something else.

Thanks, I was worried it was hardcoded and impossible to disable

I found another one like that about a month ago and made a bug report: https://bugs.kde.org/show_bug.cgi?id=410552

Now you've found one so you might want to add a comment to that report.