Certain parts of the game haven’t aged well, but there’s no denying that Vaas was a wonderfully done villain. He’s a great test case for the “a good villain can’t be absent and mysterious” argument. Most of the memorable villains in gaming have been nearly omnipresent; Vaas, GladOS, Andrew Ryan, Handsome Jack, etc…
All of them are good villains because they are consistently present. They have enough screen time to actually develop into full fledged characters. They’re not just some dark and mysterious overlord, patiently waiting in the bottom of a dungeon for you to come fight them. They’re persistently in your face, interacting with you. Even if they’re not actively hindering your progress, the fact that they have a continued presence means their eventual downfall is that much more satisfying.