Hi Pat,
I helped a friend last year with installation of his Vetus bow thruster, and whilst I haven't yet found specific information regarding your particular bow thruster, if it's anything like the drawing shown in the screen shot photos below, than you should be able to remove the motor without fear of water ingress.
The important thing is not to separate parts 7 and 8 which have the tunnel wall sandwiched between them, but simply to remove the motor from part 7. The drawing suggests there are four bolts which should be undone which secure the motor to the intermediate flange(part 7) or entablature, on top of the thruster tunnel. I don't remember specifically how many bolts were provided to secure the motor to the entablature on my friends boat, and his was a brand new installation, so things may have changed a little from when your bow thruster was installed, but I'm guessing not by much.
The motor shaft connects through a coupling (part 6 in the drawing) to the drive shaft for the thruster, so that connection which is located within the open space of the entablature will need to be loosened before the motor can be lifted off. You will of course also need to disconnect the electric cables from the motor terminals.
It's an easy enough job so long as you have enough space to get at the motor.