battery management system

Can the thruster cause the BMS to disconnect the batteries

Yes. Thrusters are heavy consumers, and they may create sudden peaks in current draw, which again may cause the BMS to disconnect the batteries if the thruster draws more current than allowed. If this happens in the middle of a maneuver, you would be left without thrusters and may lose control of the boat.

Most engineers would tell you that it is not ideal for connecting the bow thrusters to a service bank protected by a Battery Management System. 

Hence, Sleipner recommends that the thrusters be connected to a separate battery bank (that is not lithium) without a Battery Management System that can disconnect the batteries (and consequently the thrusters).

Disclaimer: Ensure battery/energy source is installed according to CE/ISO current rules and regulations and by licensed electricians.