The doors should cope with water entering them anyway, it should just drain out of the drain holes in the bottom.
I can't understand what you've said about the speaker wires, but is it possible the wires are catching water (that would normally run to the bottom of the door) and diverting it out through a grommet so that it comes inside? it might be as simple to fix as pulling a little more cable into the door to allow the water to drip off the wires into the bottom of the door so it can run out as normal.
'07 Touareg V6 TDI with air suspension
'98 Mk3 Cabriolet 2.0 8V
'99 A4 Quattro 1.8T
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