They won't run hotter if the cooling system is up to the task. If you build a 600 hp engine then you need a 600 hp coolant system. Doesn't matter if it is a stroker or not. The coolant system has to have the capacity to cool the engine when it is making power.
I put a C body radiator in my Duster when I installed the low deck 512. That setup worked great. The thermostat would open up at 180 degrees and the engine would stay right around 180 degrees while I was driving the car. Only time it got above 180 was on super hot days if I got stuck in stop and go traffic. The temp would climb up to 190 or 200 when the car was stopped but would drop back to 180 once the car was moving.