This issue still exists in Mojave but here is why

You NEED to make sure that you DO NOT run CleanMyMac X, or any other version, if the default ignore list is not populated. It will delete so many system files that you will be in MacOS He double hockey-stick for a LONG TIME, Trust me. Its taken me 2 years to figure out why MacOS would not stabilize until I realized it was deleting all PLISTS, CACHES, Logs, and with Mojave, and cloud integration, it deletes so much that the system becomes VERY unstable, even causes issues with the SSD.

I am currently backing up my computer for a total rebuild for the 20th time, and figured this out on my own, and came across this thread.

So the question is "is this still the same in Mojave" the answer is, YES ITS WORSE.