I think it's safe to assume that the ships are so slow because if they were much faster, the capships wouldn't seem very impressive if you could just zip from one end of a Sathanas to the other in a matter of seconds
So I guess that's one of the cases where realism had to go in favor of gameplay. Not that realism is too much of a concern in a spacesim at any rate
Anyway, we can just decide to imagine that the speed we see is the relative speed at which the ships are capable of meaningful manouvering, so they'd really be able to go much faster but at greater speeds it would take forever to change their heading. Thus, they can well be going at 200 m/s, but if the capship they're attacking is going at 150 m/s in the same direction their relative velocity is only 50 m/s. And if they were closing from the opposite direction they wouldn't be able to brake in time to attack so they got a computer controlled speed cap that keeps your relative velocity at a level where you can actually manouver. Not sure if that makes any sense, but hey, there's gotta be
some reason why their max speed is so low, and that's my idea for why
[Edit] As for planetary flight, I think you're right that the planets would have their own atmospheric fighters. Regardless of speed, most of the spacecraft in FS2 are anything but aerodynamic. And while aerodynamic lift might not be needed for them, the drag from their shapes would make them handle like bricks, and the friction due to that drag would make them burning hot. The Ulysses might do ok since it's got a fairly slim and low-drag profile, and some like the Myrmidon or Herc II
might get by since they either aren't too bulky are shaped somewhat aerodynamically. But most I just don't see even trying to enter an atmosphere. Especially the Ursa
