I'm wanting to use the Thieves Guild vault to store different kind of "loot" that I get throughout the game. Things such as gold ingots, gems, etc. I really wish we could drop gold coins but its not possible on the 360 (I'm sure there's a way to do it on the PC). I'm wondering though, is this a safe thing to do?

After its almost completely empty and has a ton of empty (and open) chests to drop stuff into.

Will new things ever get put into these chests that will mess up what I put in there? And will any of the other thieves that lurk around the cistern take anything I leave in their? I'd really like to deck this out. I want tons and tons of stuff in there.

I wondered the samething. Even at the end of the quest line you still cant. I was disappointed by it.

From my experience the vault never gets refilled.

Also, It wouldn't be the best place for storage because if you close the doors I'm pretty sure you can't open them again, says you need the key.

I know someone can answer this. I never had to do the spoiler thing so I am not sure how. I think I do but I dont want to take a chance. So all I can say without spoiling is it always says you need a key.

According to http://www.uesp.net/wiki/Skyrim:The_Ragged_Flagon the entire place (besides the training areas) are safe. I'd use the other chests personally. That's just me though.