Yet another classic engineering conundrum.
The efficiency of eliminating shafts and whatnot is highly appealing, but then there are the downsides noted above, as well as the motors' greater susceptibility to damage.
Then all the opinions, educated opinions, and trading-off begins.
I think there isn't a single right answer. I agree that bicycle hub motors are great. I think that if the vehicle sees very smooth and clean roads, hub motors could be the best choice. In filthy, bumpy conditions- which are also more prone to damage- I'd want an inboard motor with shaft drives. And/or: is there a lot of accel/decel or are the trips predominantly cruising? And then there is, waddya gots to work with and how much do ya wanna spend? Do you want some sort of transmission tween the motor and where the rubber meets the road?