Just tested it with two MKVs:
One containing a video and audio stream
One containing only an AAC audio stream.
In both cases, MusicBee opened the file in the default program associated with MKV files.
You can specify a different program to use, but it doesn't appear that MusicBee will try to process it at all.
-edit-
Renamed the audio only track to .mka and MusicBee did play it internally.
Bee excellent to each other...