I'm now so sick of this crap happening I'm keeping a running count as I play. Anyone else with a similar annoyance please feel free to post and edit your post as you play. Please note, however, I'm only doing this for the empty Secure System missions you get where there are no NPCs at all.
Missions given: 7
Missions that were empty: 4
Missions that worked: 3
7th Mission meant losing all but 1x phaser and my quantum torpedoes on my science ship vs the Elite battleship... again it seemed to suffer a loss of attack power / weapons too.