The wiki lists approximately 100 types of fleet ship (note - I did not count them, I copied the list into Word, looked at the word counter, and divided by two on the assumption that there were roughly two words per ship name). Since each fleet ship has four to five mark levels, each of which usually has a unique model, that would give about 400 unique ship models for fleet ships alone.
There are also about 15 unique lines of starships, which would add roughly another 60 relatively unique models if the models for starship mark levels are unique.
The \Images\Ships folder in the install directory includes 1068 files, although some of those are color masks.
Based on the above, I would guess that there are roughly 700 unique ship models in the game, but beyond that guess I could not tell you, and that guess probably includes things like turret and command station models.
