Board schematics are here (see page 17):
USB power is controlled by current limiting switch HPA00615DRVR http://www.ti.com/general/docs/suppproductinfo.tsp?distId=26&gotoUrl=http%3A%2F%2Fwww.ti.com%2Flit%2Fgpn%2Ftps2553
Specifications on that switch say that it will shut off in the event of reverse voltage, which is defined as OUTPUT side voltage EXCEEDING INPUT. So its using a voltage comparator in order to determine that. Obviously, the threshold for reverse voltage is not being reached.
Now if you go back to page 2 of the hikey schematic, you can see what is all connected at SYS_5V, which includes the LEDs.
Now you say that when it is still powered, that “Hikey is not getting detected in device manager.” (not sure what “device manager” is, but I’ll assume that it somehow tells you the output of
lsusb or equivalent). You can see also on page 2 of the hikey schematic that the PMU is powered from VDD_4V2, which is separated from SYS_5V, so presumably the major components of the board (SoC etc.) are actually powered down at this time, which is why it is not detected.
In other words, I don’t think that you need to worry about those lights being turned on. If it really bugs you, you can always cut the +5v wire out of your USB cable.