RE: Shogun 400
Because you are just hovering there is no air passing by the motor to help cool it. Once you begin forward flight it will running cooler. I believe a brushless would run cooler.
The real problem is you are running Lipos on the brushed motor which means you should have a dropped the motor tooth by one to a 9T. Lipos introduce a higher Amp and Current opposed to a Nicad/Nihm.