I can’t list them because I don’t know all of them, but the general rule of thumb is that the farther away you get from the standard of 1000 for CFF, the more likely one of your end-users will encounter problems using your font on their device(s) due to the variety of apps, operating systems and device drivers.
Others here can give you more specific info about the problems.
Are you still talking about width/height of a glyph or UPM? If I put a 5000 units high logo in a 1000 UPM font, what other pitfalls are there other than cursor issues? And can I cure them with setting the Bbox to fit normal glyphs?
I assumed you were talking about UPM. I can’t imagine why you would want to put a 5x-size glyph into a smaller UPM although the Type 1 spec does allow for a +/-2000 units outside the UPM. It’s just not a usual way of doing things.
As to your second question, I would say no but others may have a better answer.
IIRC correctly 5000 was the number I ran into years ago that would keep a glyph from appearing in MS Word. Sadly, this is another important bit of information lost because Jared refuses to do something with Typophile.