All ships have to go though CBS for approval for inclusion in the game, including even canon ships.
Basically, each Tier has 3 catagories of ship, each catagory has a canon design (except Tier 5 which hasa Cryptic design), then each catagory comes with a couple of variants of that ship. The saucer, hull, pylons, nacelles and mission pods are interchangable between these variants, hence why they all look so similar, otherwise it would be difficult to get them to stick together properly.
Most of the 'new' ships were actually designed by Ryan Dennings and John Eaves for Perpetual Entertainment when they had the licence, Cryptic inherited all of the assets from that company, including the ship designs.
Some of the ships arn't actually as bad sa they appear from the side views, and its worth noting that ones mans junk is another mans treasure, there are alot of people flying ships I would be seen dead in, but they think they look awesome, its all a matter of taste at the end of the day.