Here is two other thoughts about your missile boat: If the magazine explodes, the ship is destroyed. Also, if the missiles run out, your ship is kind of useless until it gets into ramming range.
Sometimes, it is best to design a missile boat only to shoot two or three salvos, with the minimum armor to survive that.
Also, if you're going to create such an armored ship, it should have beam turreted weapons, so it can fight after the missiles are gone.
The Magazines have only a small chance of not being ejected, have 3 HTK each, and before being hit, they need to pierce through the armor.
About the speed, I was fighting precursors, which I hadn't much hope to be faster, so I designed this with the expectation that my enemy out techs me, and therefore will be faster than me, unless I put an unreasonable amount of engines, so it's intended both to be able to take the hits, and have a range that will have the enemy inside, even if they're faster than me. If I'm out of missiles, I'd run away till I can reload. I might give them some colliers if the fleet is intended to act in a long war.
Also, on the question of FACs are a notable weakness of my design, specially if they're armed with mesons. I have a size 1 anti ship missile to help me deal with it, but even so, it's not enough for huge amounts of FACs. I'm courting designing one.
Beam weaponry would means that I'd need to close in, which would be both very hard with my speed, and not intended to be done on purpose. Plus my beam weapon tech sucks a great deal.