The cron was restored with once a week frequency with manual packages update setting. The emails regarding the Cron stopped sending. Now the WHM/cPanel server load is around 0.3 and everything looks normal and is fast.
To disable cPanel updates, you should set the option to Never Update, under the Daily updates section here:
WebHost Manager »Server Configuration »Update Preferences
Updates will still run, but cPanel will not be updated. I suggest you leave the Operating System and Apache SpamAssassin updated enabled.
Sounds like the update didn't complete or has not completed properly though.