I finished the Thieves questline minus becoming a full fledged Guildmaster, but I have wondered this as well. I've started piling gems, rings, necklaces, weapons and armor into the open chests. I'm fairly wealthy now and have two homes so I don't really mind how I spend my money. In my mind, I came into wealth because of the Thieves guild-I have no problem giving back.
With that said, your suggestion of being able to use the treasure vault as a storage and display area is BAD ASS.
I'll become Guild Master soon so I'll be able to verify whether or not it stays empty, but if it does stay empty, I hope someone like yourself makes a mod to change that. It'll probably have to be a mod you enable AFTER you finish the guild's quests otherwise when Vex and others open it, they'll find it full and proclaim it empty.

EDIT: I should mention that if you include several bookcases, you'll want to make the vault MUCH larger. Or you could instead make an addition to the college of Winterhold. Story wise, it would make more sense that the mages guild holds the largest library.