I think the batteries are placed where they are in hybrids to take advantage of the passenger compartment climate controls. NiMH batteries are happiest at the same temps people are happy with, the engine compartment big swings of hot and cold would make temp control difficult, giving poor performance and shorter battery life.

The Prius has a fan that sucks air from the passenger compartment, over the batteries, and exhausts outside. The fan is variable speed depending on the battery temps.