Every time I do the menu glitch, there's like a 20% chance my whole game crashes and I have to restart it (I'm playing on Switch). Does that disqualify a run?

Oof, the switch port is rough. Crashes don't disqualify the run, you can still submit, although they are of course a major timeloss and plain annoying for the runner. There are categories without menu glitches, maybe that would be an option?