The problem seems to be connected to software... but I see it more rarely now - only on some rare occasions (Maybe indexing had to do something with it and initiated it more often as well).
Now I encounter this, for example, sometimes when switching from bootcamp partition to macOS and then shutting system down afterwards (screen goes out/lights off but I can still hear a fan for about 10-15 secs). However, sometimes it happens on simple Sierra restart/shutdown process as well (rarely and I do not know in which specific cases).
If this happens on restart - it simply hangs my mac with blank screen for 10 seconds before it starts to boot again. Normaly shutdown/restart until boot process takes only around 4 seconds.
Windows 10 on bootcamp partition shuts down almost immediately with no problems.