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I find that on products that are mostly digital removing LEDs and speakers shouldn't cause an issue. However, some analog electronics may be designed with the LED as a current path. If this is the case perhaps you can replace it with a non light-emitting diode with similar Vf

If you can open it enough to cut the led, why not just wrap the led in tape while you've got it open? That should cut down on the light leakage through the usb ports.

Put a small square of tin foil to cover the LED, and tape over it. It's non-invasive and I haven't found any LED that shine through tin foils.

You should always be able to replace them with an appropriate resistor.