Alright, well first off, I had considered that spamming them would be...too much, but I never intended to, fleets utilising all the same ship don't appeal to me. I really like the emissary, custodian, hero, explorer, warden and orca. So as you can see, some veriaty.
I think your changes are good, there are only two things I think I disagree with. I know my emissaries, explode when sneezed at, but given that they're diplomatic vessels first, military ships second, is fine. they also pack ridiculous punch at 110 (or 100 in BFG:R) points, so it's for balance. I feel like a dedicated missile boat should be slightly more resiliant, with an extra shield, or the option to buy extra hits or something, similar to the merchant. To continue the comparison, it does have more ordinance, but the squadronned turret rules in BFG:R make 4 waves much less useful. For example, while I know their turrets are better than average, I have 4 eldar escorts shoot down 2 seperate waves of 1fighter + 3Bombers form imperials, and Tau can have the same turrets Eldar have. Tack on to that that alone, a missile boat can't really hurt anything with gunerry. It can barelly hurt shield with it's guns.
The second thing is the restriction. While I agree that a restriction would be wise, i think 1/500pts is too much, it'd be almost as rare as a Custodian! I would think something more similar to the Hero restriction. in BFG:R it would be part of the FW fleet, so you couldn't use 1 protector to get a hero and a missile boat.
Those are my thoughts. I'd love to hear what you think about 'em, and if you have more suggestions. (Or if anyone has suggestions, thoughts or comments, you're invited too)