remember that in the next patch, FP are gone, replaced with deployment points. you can basicly have a huge trader fleet with some merc escort and still have place to send them into combat with your own DP
Exactly. Mercenaries should be a useful instrument if you are not specialized in combat. But if you build your own big combat fleet you'd not want to be dependent on mercs, would you? Well, you'd be, because the best way to face a maximum sized battle fleet with your maximum sized battle fleet, would be to go beyond your size limit for a short time with mercs. That would turn a potential tense and exciting battle into a one sided slaughter.
Mh, one thing that I could imagine working is that while merc ships count towards the LR of the fleet, LR does not (or reduced) influence their CR. That way it would not make sense to bolster a pure combat fleet with mercs beyond your supply capabilities since the CR of your own ships would drop, but if you have a huge trader fleet you could push the limit since the CR of your own civilian ships doesn't matter as much.
One thing that was not mentioned in the OP is that, while the client's fleet bonuses should not apply, the skills of the mercenary captain should be in effect for his ships.