They (should) replace all the connecting plumbing anyway. Its just PVC these days. It shouldn't be an issue. You should, of course, check with your contractor - but it should just be a question of which new pieces you buy for the trap and all.

Very deep (9-10") sinks are common these days. If you end up with one, make sure your main drain pipe is situated lower than the exit pipe from your garbage disposal. That was the one detail we missed, and ended up dismantling the disposal. We're fine without it, though. Good luck.

The plumbing changes are fast and cheap. Get the sink you want; the plumber will make the disposal happen. I've only had the plumber reject the owner's disposal choice once; it just wouldn't fit.

99.9% of the time, it's not a big deal for the plumber to do this change.