If you set custom-join-message or custom-quit-message to "none" it doesn't disable join/quit messages, but simply send the default messages.

Have you tried setting the message to ""? "none" is supposed to show the default messages.

Setting the message to "" give an empty line

Is this a major problem? There's no actual indication of what happened unless players check the tab list.

In some old essentials' version this bug wasn't present. But i believe that is easy to fix

If you give players essentials.silentjoin permission, and have allow-silent-join-quit set to true in config, those players won't have a message when they join.

Depending on your permissions plugin, you may also have to negate essentials.silentjoin.vanish.