There's the theory that he's hiding a private life that some people disapprove of. Some say Rush Limbaugh — of all people — told him to lie low. Right wingers supposedly protecting other right wingers from getting caught doing things that right wingers supposedly loathe.
Lefties love to think the righties they can't tolerate are intolerant.
ADDED: Here's the Gabriel Sherman article in TNR:
What is driving Drudge to seclusion? Those who know him say that part of the reason he has disappeared from public view is that he is so bothered by the media's prurient interest in his personal life...
Perhaps Limbaugh... was trying to protect a fellow conservative from attack by the left. Or maybe he simply grasped something that now appears very obvious: Matt Drudge owes his power in part to the air of mystery that surrounds him.