I haven't been back into bitcoins for a while, so I'm unfamiliar with how many coins they manage.
It seems like they're handling it the way they should with the case-by-case claims system.
I personally don't trust online wallets; I'd only use mtgox when cashing out.

Edit: My guess is that after the 90 day claim system is done, they'll resume operations (if not before then for generating and using new wallets).