Should I under-cook vegetables if I plan on microwaving them the next day?
The vegetables are likely to cook more during the reheating process, so if you don't want that you'll have to cook them less initially. They won't be the same as if you'd stir-fried them to perfection and eaten them straight away of course, but this is something I do myself when preparing meals to reheat at work.

So, basically, the answer to your question is "yes".