I know it doesn't really help you, but just in case - I'm on 10.13.2, on a Hexacore 2013 cylinder-style Mac Pro, which uses an SSD formatted as APFS. My external Thunderbolt hard disk is also APFS. Also have a 2011 MacBook Pro, which works fine too (self-installed SSD formatted as APFS).
This is the most stable my Virus system has ever been.
In which case, whatever it is, can't be that MacOS version - in the sense that it causes problems on every system.
There is an obvious difference for me though. I use Cubase and Ableton, not Logic. I wonder if you could try the demo version of Ableton and see if you have the same problem?
It'll be interesting to see if you can narrow down what's causing your problems.