The Parliament class we first see in Cupid’s Errant Arrow is 2D illustrations. It’s not until Parth Ferengi’s Heart Place that we get a 3D model.

The chaotic battle we see in the opening credits are mixed. The Romulans and Borg are 2D. Starting in S2 we add 3D Clumpships and Birds of Prey. S3 adds 3D Crystalline Entity. S4 adds 3D Breen ship, and 2D Whale Probe.

The Parasite scene is mixed. The Cerritos is 3D. The Parasite is layered 2D giving the illusion of 3D.