What happens if through some effect (such as tmnt 021 Shredder's SP) a piloted vehicle gains Earthbound/Neutralized? Specifically does the pilot stay in or get ejected or anything?

Nothing, really. It will still be a vehicle.

From the E&C at WIN:

Are there abilities that are granted by having the wheel and if so would those be unusable while eb\n?

Yes and no.

Having that symbol makes a character a vehicle, and so it would get all associated with being a vehicle.

But as indicated above, EB/N has no effect; the Vehicle symbol can't be replaced.