On the question of maximum speed, three phase drives and motors are much more able to sustain torque across the speed range than traditional DC motors, so it becomes less important to tweak the gearing for the best performance at the chosen maximum speed for the route. It may even be that the traction of the 345s is the same configuration as these but they are limited to 90mph for some other reason or simply because the spec didn't ask for anything higher.
They may also be thinking of bouncing morning peak trains back out as fast ECS (and vice versa in the evening) so more trains can do peak direction runs during the same peak. Since the peak direction service dictates the fleet size this would allow them to do more with fewer trains.
Other things being equal a bigger fleet needs more siding and workshop space and if this is available at all in the London area the land would be very expensive. So they may have to do middle-of-day stabling further from London, and perhaps even move heavy maintenance further out as Siemens have done at Northam.
For any of these situations the ability to run at 100mph and therefore use the fast lines without delaying other trains would be very handy.