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I believe the purpose of the aux water pump is to provide water flow through the engine core during the residual heat mode. If you don't use this mode, having a dead one shouldn't matter.

From the User Manual:

Residual Heating Mode
The heat which is stored in the engine is utilized for heating the interior when the engine has been switched off (while waiting at a railroad crossing, for instance). In ignition key position 1, you can alter the settings of the automatic climate control. In ignition key position 0, the system automatically directs heated air to the windshield, side windows and footwells. This function is available for operation when the outside temperature is below approximately 59 7 (15 6), with the engine warm from recent operation and an adequate charge in the battery. The LED on the button will light up when all conditions have been met.
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