Does this mean that all Fleet Ships, Starships, ect are going to be debuffed or weakened?
Relative to superweapons, yes. Basically in the past there was normal stuff and there were superweapons, and the superweapons stomped all over normal stuff (except when heavily outnumbered), and it was good. Then after a few years of balancing and raiding up some normal stuff that used to be really weak (certain bonus ships, guard posts, etc), we realized that the superweapons were often being taken down by surprisingly small amounts of normal stuff.
So the idea is to leave the relationship of normal stuff to other normal stuff the same (such that you wouldn't even notice the difference in a purely vanilla game), but let the superweapons be relatively stronger again.
Not necessarily 100x stronger than they are now, mind you; the exact ratios would have to be worked out via experimentation.