In my experience astrodynamics was always taught (undergrad) by ignoring the mass of the spacecraft entirely, since when calculating the forces the mass of the spacecraft and fuel was negligible compared to the mass of the planets.
The mass of the spacecraft, and how it changes as fuel is burned, can of course be ignored when computing gravitational forces, yes. But it can't be ignored when computing things like how much fuel is required for a particular burn to achieve a desired delta-v.
