Before release of iOS 10, extension only works with container app. There is no way to create independent extension without parent app.
But after release of iOS 10, I found that we can deploy Sticker iMessage Pack without any parent application.
So can we create iMessage App with other functionality, independent of parent application?
If yes, then can we use In App Ads for monetization within iMessage Extension ?
You can either create an independent iMessage app, or an extension to an iOS app. Note: currently, if you create an iMessage app and decide later you'd like for it to have a parent iOS app, you won't be able to do that in iTunes Connect.
In my experience you also can't load ads in an iMessage extension, and external links are prevented. So your best bet is to use in-app purchases or charge for the app to monetize it.
Yes, here is iMessage development guide. We can develop Standalone App as well as Extension for Application.