I am also experiencing this problem. An additional detail that I don’t think anyone has mentioned previously:
In the Plug-In Manager, both “Blackhole” and “Blackhole (No MIDI)” appear. Both show as successfully validated, and both have the box checked in the “Use” column.
I strongly suspect that this will turn out to be a bug in Logic Pro 10.8 when the name of 1 plugin is identical to the name of another up to the length of the shorter of the 2 names.