One of the things Ive noticed with some of these ships is the forward armor tends to be flat to the target. this opens up somewhere to shoot at, try and keep the front profile a more slanted so that rounds have a chance of missing or bouncing off (which in KSP physics is a rare occurrence). It makes for a more dependable ship. though thinking about being attacked countermeasures would be an interesting idea to deflect and make missiles change course, like a rocket firing directly into a solar panel making it smash up into debris that make it hard to shoot through. as for weapons MIRVs with a decent weight could easily tare through multiple armored plates on the side of a ship. and splintering before impact could do more damage than the same missiles fired individually. The other day i was also testing weapons that used the rocket on a ship rather than a missile type system. so a mainsail with decouplers flying infront of it. these easily got a significant speed. similar to current day tanks this firing mechanisim gives the projectile more speed in a shorter distance. though im not sure if you could fire payloads like this.