Try to look at it from a perspective view
They are hoarding lots of small shuttles they use to travel between the big ships and planet surface. Once you start unloading the weapons on them, they'll start swarming your ship and deploy bombs on it's hull using the little shuttles. If you don't manage to destroy them before they reach, you get swarmed by boarding attempts and home made bombs get to your hull and inside trough the cracks and you may have to bail out.