So I'm doing the independent thievery quest for the thieves guild and I just cleaned out Avil's castle of every item that can be stolen. So if I leave the castle and say travel to the IC for awhile will the items I took be replaced or will the castle look empty for now on?

Some chests and containers respawn after three game days, as long as you leave the area. http://www.uesp.net/wiki/Oblivion:Respawning explains it a little better. I'm not sure if things on shelves or tables respawn or not.

Food and ingredients on tables will. Anything else won't.

Correct. That castle will look bare now unless you go around dropping things and moving them around to redecorate. It is the same if you grab everything sitting out in a guild hall. For shorter games, it is not a big deal, but for longer games it may be worth carefully considering what stuff sitting out that you take. Long term thieves may be wise to consider primarily stealing items inside containers. I don't even pick up nirnroot, varla or welkynd stones anymore because they don't respawn.