Sort of, you can customize alot of ship classes to a limited degree both in terms of appearance and various slots that effect the ships capabilities.
Like for the Odyssey as long as you own the right variations you can use different parts from the Odyssey, Yorktown, Endevour, Mirror Lexington, Verity classes (because these classes are all just variations of each other). And you can use different kinds of weapons in each of its 4 forward weapons slots and 4 rear weapon slots, use different warp cores and impulse engines (a rare few of these also effect appearance, like the Borg set, although a lot if special Shields especially can optionally alter appearance of your ship).