Some great thoughts and discussion in this thread!

Pre-rendering the ship angles for a nice roll is a great technique, we have used it often.

You could consider 11 frames for reasonably smooth roll. So you have 5 either side of a center frame.

If you are planning to clean up the render to pixels you really don't need to spend long on the 3d. (1 hour of work for a quick model..)

Just enough to get the basic shape down, and extrusions for the wings.
Render it with a high ambient light in your scene.
If it has some simple blocks of colour, just cut them into the mesh and apply a different material. No need for UV Mapping or textures.

You might also be interested in our deviant art group the Shmuproom.
There are lots of other examples of nice pixel art ships you can see there.

We can chime in with some thoughts/advice..

The key to this kind of animation is an efficient workflow. This is essential to creating a large amount of frames in a short time span.

The basics involve, fast selection of colour, quick translation of blocks or layers of pixels, and cycling or scrubbing of the animation frames. Typically all on various hotkeys.

Personally we do our work with a pen/tablet, but this is not essential with this kind of art.

If you search around you may find some different techniques for animating.
Our preference is to block in the main shapes with flat colours, and get the motion right.
After this comes the cleanup, outlines, and shading.

All the best with it!