It seems like an unlikely thing to do. In the case of the Pandaboard, there's only one linear regulator enable line that controls both USB and Ethernet power. Using it cuts board power consumption by about 30-40%.
Looking at the schematics, it SHOULD be possible. On the SMSC LAN9514 chip, there are 4 USB ports and 4 USB Enable pins. These drive a TI power switch. As I don't have one, I can't test this at all, but the options should be somewhere in the SMSC driver, if implemented to turn off individual USB ports.
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Thanks xenoxaos for the tip I will have a closer look to the smsc driver! If I can't solve the problem in the smsc driver I will use one GPIO pin to cut the power on the specific USB port (hope not )