Hi Steve,

Both a rudder pickup and the 'flush' mounted one have a certain amount of drag, as has anything sticking out from under the hull.
If you have a temperature sensitive set-up (on the edge, so to speak), the rudder pickup is my favourite, as it ensures flow through the system at all times, exept when you flip the boat.

A truly flush mounted pick-up, would be a brass or aluminum pipe facing forward as a pick-up and a second one facing towards the transom as outlet, both sanded flush with the hull.
This is a pressureless system that has virtually no drag and generates flow at all times.

I use a spray pick-up on my fast electrics, where the pick-up sits in the propspray in the upper right quadrant, seen from the rear.
The propspray has an average pressure of 2 Bar, so there's always flow and very, very littte drag.

Take your pick...

The faster your set-up, the less drag you'll want, to avoid handling issues when approaching the hull limit.

Regards, Jan.