The decision of whether or not to leave the USB port's power circuit enabled when the system is in ACPI S3 ("Sleep" / "Suspend to RAM") is left up to the motherboard BIOS/firmware. It may even have a BIOS option you can configure for this purpose, to enable/disable the USB power when the system is asleep or even turned off.
However, there aren't any motherboard implementations, that I know of, that will keep the data part of the USB connection enabled while in S3 or powered off. When the CPU is suspended or off, it doesn't make sense to maintain the data link layer of the USB bus, because even if you sent a message through the bus, the CPU wouldn't be there on the other side to receive the message. But the CPU doesn't have to be on for a normal ethernet card to do Wake on LAN, either, so I did a bit of research into this....
USB controllers are usually connected to the CPU using something like PCI or PCI Express. PCI and PCI-E support Power Management Events, which are essentially what is used by an on-motherboard NIC to tell the system that it's being woken up due to a WOL. In theory, if the USB controller were receiving standby power from the PCI(-E) bus, it could then decode a wake on LAN magic packet from a USB device, and translate that into a PCI(-E) PME, which would trigger the wake. So I believe that it is possible, in theory, at a hardware / system design level, to implement a motherboard and a USB Ethernet or WiFi chipset that would support this.
I just don't know of any that do, off the top of my head.