Yes they chose not to appear.
It has been nine years since Rachel Weisz appeared in the first The Mummy. She has made quite a name for herself, and has a family to take care of on top of that. She wasn't the only one not to return for the third movie. It had a new director as well. When they finally got rolling on #III, Ms. Weisz was already committed to a half-dozen other projects in various stages of production.
As for The Dark Knight, every batman movie has had a different heroine, so it shouldn't have been a surprise that Holmes didn't return, especially given the terrible reception she received in her first performance. The producers did offer it to her though, and she turned it down due to other production commitments.
Underworld 3 was actually a prequel that mostly predated Selene's existence, so Beckinsale's role would have been limited in any manner, but she still declined to do more than a voice recording. Considering her husband was the director, turning it down must have been a bit awkward.