When Combat™ is finally complete, people will be allowed to attack the NPC transport ships?

I really hope not. NPC ships should be one of the very few things, along with Starting planets, that should be off limit to combat.

if it bleeds we can kill it

(I don't have any say in combat implementation so this is just speculation) I really doubt it. I also highly doubt combat will be a "fly into any system and shoot at everything" type of system. I think there's a good chance there'll be stipulations to prevent ridiculous amounts of pew pew pew taking place whenever it's released.