Gear ratio is independent of gear pitch. If both cars have the same gear ratio, they would theoretically have the same speed. (In practice I suspect 64 p might be very, very slightly faster, due to less friction, but I've never tried. I also suspect you wouldn't really feel it unless you were some kind of pro.)

Personally I'd stick with 48p, unless you are running a pan car.
48p is also stronger and easier to set mesh if you have bad eyesight like me / are new to rc.
Seeing that you already have 48 pitch gears, why not save yourself the money and spend it on hopups/electronics?