I started tracking my profit and loss when I started reading multiple posts saying missions netted a loss. My goal was to track 100missions, but I stopped at 80 when I realized that it is not a loss over the long run. At 80 missions, I had averaged ~550 credits per mission between credits and schematics I sold. 550 credits every half hour isn't all that great, but it's a steady flow of income nonetheless for companions that otherwise would sit there and do nothing.
This is with slicing maxed and running the highest missions possible with companions that are nowhere near being maxed out in affection yet. With higher affection, I'm told that the crit rate for the missions goes up considerably. I have a guildmate that is just shy of a million credits running slicing missions and gathering boxes up to level 34, and he swears its because he maxed out the affection on his companions first before sending them out to slice. I've read different theories on affection, but he swears that the higher affection produces way more crit'd returns