ATMega32u4 (Leonardo) Serial Baud Rate
I'm not sure if the concept of an "actual baud rate" is really meaningful in a pure USB connection.

In my experience, the 32u4 is faster than the 328p at serial-heavy tasks. There is no intermediate chip, and USB has much larger hardware buffers than the serial port does. I don't know how much processing you're planning to do on your data, but I would expect that a 32u4 can process serial data pretty much as fast as you can generate/process it.

On the host side, it seems to me that there is very little difference in whether the "virtual COM port" has an FTDI or a 32u4 on the other end, so I don't see why one should be faster than the other (though admittedly they go through different device drivers).