The ships that are being used could generate their won gravity. Even low gravity environments provide a substantial defense against muscle and bone loss compared to Zero-G. The easiest means to do this would be having a portion of the ship constantly rotating, especially if this is the living quarters. I personally like the idea of a central stationary "engine" around which the living portions revolve, and thus simulate gravity, although there are a variety of different options available.
If your ships are never going to enter atmosphere, or have a much smaller shuttle with which to do that, your options for design are limitless-- as a rocket shaped craft would travel in the same manner some silly looking triangle-shaped ring formation hodgepodge monstrosity would.
Otherwise, if you allow yourself to play around with possible biomedical advances, you could have injections or other such means of retaining bodily mass-- at least for the short term.