I had the same opinion initially, but then reconsidered. I concluded that if there was a hole in the case for the micro-USB connector, that there was a likelihood of applying lateral forces to the connector if an attempt was made to open the case with the cable plugged in, and that this would be bad given the known weakness of the connector mounting.

However, a hole for the LED would be useful, although given the degree of slack in the case closure (at least in my case), the front cover does seem to move around a bit, so the hole would need to be fairly large.