I have dozens of customers with wooden framed windows, I only clean the glass on these, the reason is, I cannot see if the frames are leaking sap and when you spend £40 for a brush head the last thing you want is a knackered brush.
But with regards to pure water rotting wooden frames is a myth. damp environment is the worst culprit for rotting the frames. If the frames are cracked then the water that runs down the window will sit in any of the cracks, then soaks into the wood.
Matt