We've got a similar, albeit not much longer, [url=http://www.guildwars2guru.com/forum/what-happened-menziesi-t10523.html]thread currently running in the GW2G lore forum. His most likely current hideout is probably either some part of the FoW we can't reach... or in some dark plane like the Ravenheart Gloom.
Konig made a good point there, though. We've had foreshadowing that a being of darkness might be approaching Tyria (a hint has been dropped that what the Mad King's Court is attempting might be suborned by another, and some "coming darkness" seems to have Balthazar's followers spooked. There's also some postshadowing in the presence of the Shadow Behemoth guarding the ruins of the Temple of the Ages in GW2. I'm guessing that one way or another Menzies is still a going concern, he's just lying low for now.