Did you by any chance manage to solve this? I seem to have a very similar issue. For some reason docker seems to spike to 100% cpu usage very frequently and it can last for hours. The docker containers and the VMs seem to be working ok (albeit with a noticeable slowdown), but the web gui and ssh become unresponsive.
After some digging in this forum and netdata I found that the bottleneck seems to be iowait (up to 40-50% when this happens) and it seems to be connected to the flash drive being read constantly:
# inotifywatch -r -t 30 /boot
Establishing watches...
Finished establishing watches, now collecting statistics.
total access close_nowrite open filename
88538 88493 23 22 /boot/
897 299 299 299 /boot/config/shares/
296 114 92 90 /boot/config/
Any ideas?