I just ran Stealth A and got a flak 2 for the very first time, and the boss hacked my weapon's systems.
Basically hacking the weapon systems isn't that big an issue if your weapons don't have a long charge time, however for the flak2, it was absolutely crippling because it would NEVER get a chance to shoot. halting their charge and saving it for after the hack/cloak would accomplish nothing, because it could never get charged once to begin with.. it'd charge to half, boss would cloak, boss would hack, become empty. charge to half, repeat.
I didn't have a hacking bay of my own, nor did I have a transporter bay, nor did I have any drones....I had mind control though, and while my original intent was to mind control the missle dude until I could mantually destroy it (and kill him), that only led to a perma stalemate. So then I changed tactics and mind controlled the guy manning the cloaking bay, in turn he'd damage it partially before other crew came there to kill him, and that shorter cloak allowed me to charge my flak2 faster than the hack would deplete it (slightly, it would still take like 4 cloak/hack phases before it oculd pull off a single shot). This took along time, and the boss was whittling away my health all the while (since I couldn't disable or destroy anything during this hack/cloak fiasco)...But in the end, I managed to kill off that missle dude with my beams, and once he was down, I could focus my efforts elsewhere and the battle turned around...I had 1 hull point left.
That said, hacking the weapon bay is only a big issue if you have really slow charging weapons like flak2, glaive beam, etc. And even then it shouldn't break your game unless you have no mind control, OR hacking, OR transporter, which I strongly do not suggest. I suppose even a drone bay would work too since they can attack independent of a weapon hack.