Let's not forget guys, that the primary defense of a fighter is to not get hit.
As for the lack of internal missiles, while officially the VF-25 has none, it seems that Gilliam fired 3 missiles at the Vajra red during Episode 1 broadcast. It's at 21:21-21:22 played at normal speed, smoke trails and rocket burn are visible and if you go frame by frame you can even see a missile body.
What I'd give for official stats.
Also, just because the VF-25 is the next gen fighter after the VF-171 doesn't mean it'll have a PPB. Consider: if pilots are going to turn it off most of the time and not use it unless they want to make their glowing PPB Punch attacks, then you might as well remove the PPB and slim down the design to mount a 3-mode Full Armor system, and give the pilot an EC blade for when he wants to go melee.