Running dual cooling will never hurt a ski. In fact it helps tremendously on a stock motor. It can be set up many ways on a stock motor, just gotta do some homework.
I would absolutely run dual cooling on any motor and also run a dedicated line to the exhaust pipe. For example, if you have a dry pipe or wet pipe, one cooling line that comes in will split off and both will feed the motor. The second line coming into your hull goes directly to the exhaust pipe. This keeps the motor and exhaust systems separate of each other in case of an overheat, you will only overheat one cooling circuit and not both. It also just provides better overall performance. Water routing can be done in many different configurations.