Just picked up a schumacher 15/10/2 ship and shore charger.  According to the manual deep cycle batteries are to be removed from the boat before being charged.  Anybody know why schumacher recommends this?  

Im pretty sure its for safety reasons.

Not sure.  I know that I shut off my main breakers before charging.  The dealership recommended it to prevent any surges from damaging the electronics on the boat.  I believe Minn Kota recommends shutting off the breaker and/or disconnecting the batteries before charging for the same reason.

Liability reasons I'm sure.  

Like others have said probsbly to covet their back sides. I know on my older Champion I would just disconnect all the wires to the boat on the the batteries and charge them in the boat.

Liability.  Charging a battery too hot in a confined space can cause the fumes to build up so when you disconnect the charger, the ark can  create nice explosion.  I've seen more than one battery exploded by people fast charging them with a big shop charger and have them explode when they disconnect the clamps.   That's also why you should never charge a battery with the caps off.

Charge at the proper rate, approx 10% of rated capacity, leave the caps on and the cover open on the battery compartment and you should be fine.  If the battery/s are created fumes that a readily noticable, check and see if the case is warm, you need to check you batteries water level and check their condition, they are probably going bad.   I hot climates, you may have to reduce the charge rate a couple of amps.