Hi. No, I think you have the wrong end of the stick. The number of ports on the motherboard doesn't matter as far as the case is concerned.
Typically a motherboard has both USB ports, and USB headers. The ports will be rear facing when installed. Here is a picture of a random motherboards selection of rear ports, with the clip in I/O shield (supplied with all motherboards) underneath. The ATX standard defines both the position of the ports on the motherboard, and a cutout size for the I/O shield of 6.25" x 1.75"
An ATX compliant case will have a 6.25" x 1.75" cutout for the I/O shield to clip into, and when the motherboard is correctly installed, the ports will line up with the holes on the shield.
The other category, USB headers, are bare pins on the motherboard. USB 2.0 (9 pin) and USB 3 (19 pin) headers respectively shown below:
Most cases come with front USB ports which wire to these headers. One header will connect to two USB ports. Most of the time, there are more headers on the motherboard than you'll need to wire up the case. You don't need to use them all. In fact the headers can be used for other purposes such as for connecting memory card readers, or even lighting control modules..