Surely if you power it down so far that it's virtually unplugged, there isn't anyway you are going to be able to boot it up remotely?
If the PC is shut down, the enabled/disabled status of the USB port is irrelevant, because there's no OS to look at it. You've got to have power or you can't turn it on, and if you've got power, your USB will be live. There may be a hardware solution with extra kit, or maybe there are some systems that do allow this, but I don't think yer "bog standard" PC can be made to do it.
Why do you need to shut down the USB ports anyway? If it's to power down connected equipment, I would have thought that anything drawing enough current worry about would have it's own power source which isn't going to be shut down when the PC shuts down. (Unless you PSU has a switched periperal socket - haven't seen one of those for years.)
There may possibly be a remote controlled UPS on the market - I'm sure I've seen one somewhere. That may be a solution.