This doesn't make any sense. If they were using btce for their liquidity and to execute orders, didn't they just lose all their btc/usd?
Definitely (at least pending any refund from BTC-e). I imagine the same goes for many legitimate brokers like FXOpen, AvaTrade, Plus500 and others who were using the exchange for liquidity. The ties between BTC-e and xBTCe go deeper, though, and this is more about distancing themselves...
Not necessarily. Maybe they owned to BTC-e. It all depends on total trading gains, losses, deposits, positions, margins......... And since all those brokers are high profile with over 100b$ in monthly trades don't be surprised if they had an agreement with BTC-e that included bank escrow account for situation that actually had happen.