Wow I had no idea. I don't use the 0-9 buttons. Thanks for the feedback! I've also noticed that the T key on my keyboard stays highlighted after picking new research and that some things like signal wire and copy icons don't show up next to the cursor with the HUD hidden. Seems like a lot of stuff relies on it being visible ):
I have plans to try and make the vanilla UI transparent so it can still be used with a smaller risk, but I haven't figured out how yet.