Star Trek Online is a game that's being built upon one of the most popular sci-fi IPs of all time. As such, gamers have certain expectations of the title, particularly when it comes to the ships they'll be flying. As with the Star Trek films and shows, the game will stick to certain ship classes and configurations, but the developers at Cryptic Studios also need to allow for customization within that system -- everyone wants to fly something that's unique in some way. Something that's their own. This customization was the theme of a recent Star Trek Online dev chat with executive producer Craig Zinkievich.
Ships in Star Trek Online will have defined purposes, with Escort (cannons, heavy attack rating), Cruiser (general purpose, large crew), and Science vessels (emphasis on deflector dish 'powers') to be in the game at launch. Of course, you'll be able to modify them in various ways. The producer explains that the customization options won't allow players to drastically alter the look or silhouette of any of the ship classes from Star Trek canon, but you'll definitely have options within your chosen configuration.
Zinkievich breaks down these ship modifications into two basic groups: cosmetic and functional. Cosmetic changes can only be made while docked at a starbase, and can be anything from altering the shapes of windows to what escape pods look like, but won't make apparent to others what underlying technologies your ship is set up to use. Functional modifications, on the other hand, can be done on the fly in space, and allow for changes to your weapons and defensive systems.
The STO dev chat with Craig Zinkievich addresses other facets of the game as well, such as the various 'classes' available within a ship configuration. If you're looking for more details about what will be possible with ship setups in Star Trek Online, this latest dev chat transcript should have what you're looking for.