The hybrid system of the toyota's are integral to the gearbox. You can not have one without the other. So on the Aqua S '11 swapping the gearbox for a manual, will mean a loss of the hybrid system.
Each Manufacturer has different ways in which there hybrid system works. (read below for toyota and honda systems.)
The Nissan has by the sound of it, has motors built into the wheel hubs on the front "The torque vectoring of the individual front motors on the left and right..." (
http://www.gran-turismo.com/us/products/gt6/vgt/) and the engine drives the rear wheels in a conventional manor. It does also say on that website that "[Nissan VGT has a]high performance hybrid FR-4WD system with a V6 twin turbo engine, combined with 3 motors." I assume from this that there is a third motor probably built in the flywheel like the Honda IMA system, which would also explain the KERS esque boost that is available.
One thing that has just occured to me, In theory unless your driving slowly in GT6, the hybrid system should not kick in and would probably be a hinderence racing due to the additional weight.
Also just found this
http://blog.toyota.co.uk/how-does-toyota-hybrid-synergy-drive-work#.VAzWIGP1q-0 for anyone intrested in further reading.