Personally, I think they should stay emptied once you've killed everything in them. It adds to the realism of the world. There's over 100 in the game, so you're not going to run out of them in a very short time. Respawning dungeon enemies really isn't necessary in my opinion.
How many of them are fit for level 50 players? the majority will be lower levels, say they uses level 1-10-11-20 to 40-50, 140 dungeons gives 28 high level ones, now around half of them will be small 15 minutes ones, you would run through most of them getting up to level 50 and it will be few left.
The lack of high level content is actually my greatest fear for Skyrim, no spellmaking and just lame default spells, Morrowind magic was more broken and it was very good. Lack of high level content was a worse problem in Morrowind.
Yes make the respawn time longer, 7-14 days fixed (perhaps random?) and then 1-2 days without visiting the location. not the three days without visiting.