Some pilots give the wing a bonus if they're on a wing; pilots with Lone Wolf skill benefit from being alone. Since for the majority of the game we don't have a full team (unless you add Goblin Wizard's Mothership mod and hire extra pilots) yes, most of the time it's faster to let everyone fend for themselves.

Yeah, unguided missiles miss a lot. As you've observed they're pretty much useless unless against a target that isn't flying around. Even before I modded them I pretty much ignored unguided missiles except for the 32-pack.

The game engine is pretty inefficient so lag in battles is unfortunately to be expected. There's a no-fog mod which may help some players a bit (e.g. those playing on laptops), but generally large battles will always be somewhat laggy.

Explosion distance is defined in \Data\Game\Rockets.xml, simply edit the explosion_radius values for the various detonators. As others have observed, missiles are more of a pre-engagement weapon - it's too easy to kill yourself when they go off point-blank in the middle of a fight. Check out my missile mod if you still want to use missiles as in-combat weapons.

Edit:
It's possible to add bonuses while pilots are in a wing. This is done simply by adding extra code to the scripts checking perks to apply passive skills. All you need to do is add a check not for a perk but for presence of more than 1 pilot in a wing (a lone pilot is considered a wing of 1). This is how the Lone Wolf skill works btw.

Assuming being in a wing confers a feeling of safety I'd say a piloting bonus would be realistic - especially since we've seen that pilots often don't attack the target because they break off the attack run to maintain wing cohesiveness.