As long as your missile can reach out to 50m km, that first design is fine. At that range, they aren't likely to see the fighter. I tend to designate that as a bomber, really, given the speed and range of the MFC/Missiles.
Take a look at the armor DAC, it will show you that your current armor is 3 boxes wide, and two rows deep. Which means if the armor absorbed 100% of its capacity (not the way to bet) it will stop the first 6 points of damage. Everything after that goes internal. Even if you add more armor, each new level of armor is only 3 more points of damage soak, max. Most of your internals are likely to be 0 or 1 HTK (hits to kill). Basically, don't expect a fighter to take damage and make it back. Raw speed (my 100 ton interceptors go 37500km/s) and being small enough the enemy can't lock onto them at range are what keep a fighter alive. Dumping the armor will give a bit more speed.