What is the effect of remapping ports on a USB hub
As the datasheet explains, logical port numbers have to be assigned consecutively, starting at 1. If you aren't using all of the ports, and one of the unused ports isn't at the "end" of the physical port numbers, you have to use remapping to put the active ports back in order.

For example: Let's say that you're making a 4-port hub, and, for PCB layout reasons, you have to use physical ports 2, 3, 6, and 7. Port remapping would allow you to remap these ports as logical ports 1 through 4, by setting:

PRTR12 = 0001_0000 -- physical port 2 = logical port 1, physical port 1 = disabled
PRTR34 = 0000_0010 -- physical port 4 = disabled, physical port 3 = logical port 2
PRTR56 = 0011_0000 -- physical port 6 = logical port 3, physical port 5 = disabled
PRTR7  = 0000_0100 -- physical port 7 = logical port 4