Steve,
The battery "cut off" switches do not cut off all battery feed circuits. On most coaches, the main 12 volt power supply circuit for the inverter does not run through the cut off switch, therefore your inverter control will still be powered with the switch off. Also the power supply for your ECM (engine control module) does not run through these switches, and the continuous 1 1/2 amp draw from the ECM is the primary reason for dead chassis batteries in coaches that are stored.
Apparently your Aqua Hot is either wired to the inverter feed or it is wired directly to the battery. It is probably wired directly to the battery because that is a practice that some techs use in order to reduce low voltage alarms/shut downs.
As I have stated many times before on this forum, if you want to disconnect either battery bank, remove the negative battery cable or install a HD Marine knife switch at the battery terminal. A word of caution, if you install a knife switch, be sure to use one that has an adequate amperage rating. The Wal-Mart type switch will not work.
Gerald