You are correct, there is typically a 12 system and a 48 volt system. In the newer electric golf carts they use a (in this case) 48 VDC to 12 VDC converter. I am guessing that this has failed, and the flash that you are seeing is the converter shutting down, either due to a short or that is cannot support the load due to a failure in the converter.
If you are familiar with the electrical system you might be able to isolate the converter, and connect a FUSED 12 volt battery to the golf cart 12 volt system where the converter normally connects. then you could start testing the various circuits, I would start with a 10amp fuse and ONE circuit at a time. I have small lead acid 12 VDC batteries that would be suitable, and fused test leads, so I may be able to help you.
The DC/DC converters typically have built in circuitry to detect overloads and shut down the converter, and this may have been damaged by the water. This would explain a lot of what is going on. If this is the case, the converter would need to be replaced.
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Pennsylvania, for 60+ years, most recently, Allentown, now TV. 
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