Technically, no, there is not a huge difference, 9hp to about 15hp, mostly done by increasing the engine speed, but maximum torque is still achieved at a lower overall RPM, so the horsepower at the peak torque is just about the same.
Operationally, there are some big benefits, 12v-negative ground, alternator, distributer, key start, etc.
I have owned several older Cubs, and one late model, 1977 Cub. I would have sworn that it had more power and started easier than any of the others I've had, until the 1951 that I just restored. It is all original, 6-volt system, 9-hp engine, and I would bet that it would give my 1977 a run for it's money. The down side of the 51 is all of the positives noted above, 6-volt instead of 12, starter/generator, etc.
Basically, I think it comes down to preferance and what you can find. I actually think that a well tuned older Cub will perform just as well as a newer cub, and most folks would never know the difference if you blindfolded them.