I use Bartender to manage the gazillion apps I own. It has the ability to hide icons by default.
With Clocker, I find it to be extremely useful but only on demand via a keyboard shortcut. (I don't need to see timezones all the time.) Bizarrely enough, the shortcut doesn't activate unless the icon is visible. I haven't had this issue with other apps such as Fantastical or ColorSnapper.