This topic may eventually be moved, and I also urge you to look at the link that Spoony posted, but I can answer a couple questions.
Ships in Nova can indeed be put into plug-ins and reworked, but there are basically two parts (not literally, but if you read a plug-in guide you'll understand all of the different resource types): One is the graphic, which you would need some kind of graphics editor to change. The other is the resource file, which contains all of the information about the ship.
Most plug-in editors will let you change the second part, the information, quite easily. You can increase the speed, give it extra shields, make it come with different outfits, make the weapons come out of different places, anything you want.
Changing the graphics however, requires either manipulation of the ship graphics in an image editor, or a complete re-working of the model itself. Nova doesn't use 3-D models of the ships, instead it uses a grid of images created from a 3-D model. Changing the graphics as you wanted would be difficult, since you'd have to work with each image separately. Creating a new model, though, would also be difficult, since you'd be working from scratch, designing the thing from the ground up. Neither of those are impossible, but unless you're going for a simple hue shift graphics work can be quite difficult. Of course, if you're good with modeling, then there's little stopping you.
On the whole, however, check out the Dev forums. There's a lot of really good information there that can help you design a plug-in and to understand all of the different resources and how they work together to provide a seamless experience. It may look complicated, but everything is fairly simple if you break it down and focus on one specific thing at a time.