Yes. That's the entire point of having a futures market - generally, the producers of a commodity will be net short the futures contract in order to de-risk their productive investment. Buying a mining rig trades todays dollars for future BTC. Shorting a BTC futures trades future BTC for todays dollars.
These will be derivatives, not actual bitcoins. When you enter a contract you will only care about the price level of the Bitcoin Reference Rate, the contracts aren't holding any actual bitcoins, so there is nothing to hack and steal.
I'm not sure if that's accurate though. If a large quantity of coins disappeared, surely that would have ripple effects through to even the most convoluted derivatives?