It does not matter at all IF you plan to use standard mechanical HDD's - that is, the ones with spinning platters and moving heads. The speed of the mechanical components in those unit means no mechanical HDD can deliver data as fast as the speed of the SATA II (more properly, 3.0 Gb/s) communication interface. So an even faster interface makes no difference.
This is NOT the right answer if you are planning to install a new SSD. Some of the newest of these CAN work faster that the SATA 3.0 Gb/s data transfer rate, so they really should be used on SATA 6.0 Gb/s ports if you have them. But even if you don't, an SSD on a SATA 3.0 Gb/s port will operate at the max speed of that port, and be significantly faster than any mechanical HDD. That is the backwards compatibility feature of a SATA 6.0 Gb/s device connected to a SATA 3.0 Gb/s port.