Brian Armstrong, CEO of Coinbase once said in an interview (http://techcrunch.com/video/coinbase-founder-brian-armstrong...) that they are dividing their bitcoins in hot and cold wallets.
A hot wallet only contains about 5% of the bitcoins the company has. Meanwhile, the other 95% of bitcoins they're holding are stored savely in a key-split cold wallet.
Now, the problem is: if some user wants a large amount of his bitcoins out of coinbase, the guys owing their part of the split private key need to take action to transfer that amount of bitcoins from the cold to the hot wallet, assuming the amount is > 5%.
So what I think "Vault" does is give them a better architecture for planing and organizing their hotwallet-coldwallet-process.
"To complete the Coinbase Vault offering, we will be adding multi-signature (“multi-Sig”) technology in the coming weeks to enable customers to manage their own vault security."
It's not clear exactly how that will work, but if it's, say, 2-of-3 and Coinbase only holds one of the keys then it would.
Sometime in the next couple years, someone is going to come up with a relatively fool proof vault storage for bitcoins, we just haven't see it yet. (And Coinbase isn't sharing enough details yet for us to know whether they've put one together)
I didn't intend to make a conspiracy theory out of my question.
I assumed he was talking like they had just spent the bitcoin (Mt Gox stylee). Even if they were hacked, I would expect Coinbase to disclose that information--to presume that they've been hacked, lost bitcoin, and are hiding that from everyone is a pretty wild theory in my book.
[1] http://blog.coinbase.com/post/33197656699/coinbase-now-stori...