All you there must be playing super turtley if you ever build a cap of any merc ships. I have like 40 planets now so no worries about economy but I still never have so much money I'd build any more than 15 merc bombers or something. I mean, that's 1 million minerals! Why wouldn't you rather send your army to invade a new planet and rebuild the whole fleet again with that money?
A full cap of merc ships?! That is insane. Unless you are turtling with a 300% handicap, that is completely crazy.
I see some of you are saying that if you are at ship cap, you would rather send them on an attack mission where almost all of them die and then rebuild everything rather than bolster your forces a bit with the expensive mercenaries, I can give you one reason why this is not always a more effective solution, even though you may get better short term cost efficiency.
Well, rebuilding a large army takes quite a bit of time, right? Well, guess what the AI is doing while you rebuild? They are rebuilding too. Thus, if you want to (say) take out a planet, send out your max cap no merc armada and it fails to completely take out the planet, by the time you rebuild, the AI has rebuilt some too. In the late game, even just a short amount of time is enough for the AI reinforce pretty strongly. If you were willing to spend some on merc ships, you might of been able to take some extra guard posts or even the planet itself out. In this case, the AI would have quite noticeably less reinforcements by the time you rebuild (or none at all, if you managed to take the planet out). Thus in this case, it would take more cost in the long run with more slightly smaller fleets than fewer slightly bigger, more expensive fleets. In other words, in the late game, the AI may be able to reinforce faster than you can rebuild, which means one (or a few) big fleet is better than several smaller fleets.
Two notes though.
One, this only really applies in the late game. In the early game to mid game, the AI is not reinforcing fast enough to outpace your production, in which case, just sending your forces out and rebuilding 10x times instead of paying 10x for a ship might be a better idea. In the late game, they very well could outpace your production, thus the sending out and rebuilding 10x times would not be as cost effective in the long run.
Two, as many people have already pointed out, if you are not at max ship cap, it is almost never worth building merc ships. They are pretty much there only for the cases where ship cap armada still does not give you enough power to complete your objective, or if you have a ship cap armada and have plenty of money to burn.