A hundred missiles is more then enough to finish each mission. if you spamming 4 missiles at a shield generator or just locking on to four turrets on the frigates and letting it go your wasting them. use your cannons to destroy all the turrets on the frigates, 2 missiles per shield and 1 missile per engine (along with some cannons). dont bother targeting anything on the capital ships as you only ever need to take out the bridge which you need 2 protons for. ice field is probably the only 1 where you will need to use up your rockets as the sat hard point does have a bit of health.
Not sure about that 12k either. we used to get that before they nerfed the hell outa the rewards. 1 HM space mission gives a while 600 credit reward.