I just noticed on one server Spam Assassin is disabled by default (when looking through cpanel -> mail -> spam assassin). Spam Assassin is enabled thru WHM and is running. How to enable spam assassin on all accounts by default?

It probably is enabled unless the options for SA on in the users control panel is unchecked. Why dont you edit the feature list and select DISABLED. See if SA is enabled. If it is, go back to WHM and in the SERVICES option make sure SA is checked and its enabled. Then check the options in TWEAKS. Is SA enabled there?