I don't have confirmation but I'm 100% sure the clutch while be available to use.
In GT5P the clutch is fully functional aside from spec III making flat-shifting impossible, but GT5 will have damage so flat-shifting would most likely cause some wear & tear to your gearbox in GT5.
GT5 TT demo dsiabled the clutch to make the playing field even, since you can shift faster with the clutch.. I'll go as far as saying that in GT5 you can select an option so that cars that use clutches and six-speed shift always need the clutch used during races, and you cannot turn this on/off with the triangle button of the G25/27.. also, cars that use paddle shifters - you have to use the paddle shifters.
I'm sure this is in, and I would love for it to be able to work that way.