Does this battery technology also work in the high power regime for VTOL flight?
Are you referring to the X-prize, or the NASA puffin here?
Going back, lets assume your numbers of 95-98% efficiency. Then the puffin is looking between 1.2-3HP of losses that will be converted into heat (yes, I've been sloppy using HP here, but we can think of it as the rate of energy per hour). That's a good deal of energy to dissipate. Without an air scoop, the only means of heat transfer is conduction to the skin of the nacelle, and then convection of the aircraft skin to the boundary layer. Thats not a good way of dissipating heat. If you have an air scoop, you have nice turbulent air going over the motor and batteries (turbulent air is an order of magnitude better for convective heat transfer than laminar). You could probably even get away with a low drag NACA Duct