The only ships that have ever been close to unique in Star Trek are the old Constitution-class (TOS Enterprise) and the Sovereign-class (TNG movies Enterprise). During the TV show, there were only 13 of the former, iirc, and there aren't that many Sovereign-class ships. That might just be because they're so new, however.
The militaries in Star Wars largely consist of mass produced militaries, but that's due to the size involved. When you control that many star systems, it makes sense to have that many Star Destroyers. Also note that Star Destroyers of the same class as the Executor seem to be pretty rare. We only see one at the Battle of Endor, for example, and that's one of the most important battles of the period.
So Star Wars does manage to get at least one near unique ship.
The truth of the matter, however, is that a plethora of one-off ships only makes sense in two specific cases. The first is when you have a variety of different groups contributing ships to the fleet. In this case, different design philosophies would shape the form each ship took, and cause the differences (and this probably has a lot to do with it in Starlancer). The second is when the type of ship involved is relatively new. In this case, unfamiliarity with 'what works best' would probably cause noticeable changes between each of the first several ships that were built. For example, the first carrier a race builds might be a converted battleship hull. Then after a little practical experience is earned, someone points out that the fighters need a little more space to accelerate on launch, and that's incorporated into the next couple of carriers. Then someone else mentions that the catapults are nice, but sometimes damaged fighters need a little more space to land, and so on and so forth.
But when a military has been an established presence for a long time, there's no reason that the military shouldn't start to become homogenous (and your logistics people will thank you).
