If they removed the drive shaft, it's unnecessary to remove the drive shaft when replacing the pump unless the carbon ring and bellows were also replaced. Q: Didn't they water test your ski after repairs? If not, they can't know if your ski is safe to ride.
Anyway,
34(stainless ring) has two o-rings between it and the driveshaft to make a water tight seal. 34 spins with the drive shaft and 39 (carbon ring) butts up against 34 by tension from 40 (rubber bellows)
If there's no clamp (2x items 41) or if the carbon ring is cracked or worn out, water will leak. There's no reason normally to remove the drive shaft when changing the pump but if the clamp is missing then perhaps they removed the drive shaft, but that's not certain or necessary unless the carbon ring was worn and needed to be replaced while the pump was removed.
Maybe they charged you for a new carbon ring and rubber bellows (a good idea to replace these periodically), thus yes they would have removed the drive shaft to replace them.