I think one of the devs hinted at better shuttle equipment in the future, but for now all you get is the default beam array. You could always swap it ouf for a turret, though. I imagine the damage would be close, if not the same.
I used my Disruptor Dual Beam Bank but did find it a bit annoying. Stupid tractor beam got me from behind and I had to slowly turn just to fire on it. Definitely need the different weapon selections and torpedos for the shuttles. Hopefully they'll appear in-game soon.
c. the weapon is bound. (why the hell would a weapon like that be bound?)
In the case of C-Store ships, it's so you can't sell off equipment, decommission the ship, reclaim the ship, and then sell off the equipment etc. And, since you get a free shuttle with the first Romulan mission, it's the same deal.