Hi Tommy,
1) There's no special logic to link to apps in an enterprise app store, but I don't see why it wouldn't work if it's web reachable from the device.
2) If you're asking about linking to content in a DPS app, there's a "Link Reference" option in project settings, which will eventually be used for linking to an app from outside the app, but it's currently not supported. If you're asking about linking to other apps, this is standard OS functionality and I've successfully deep linked to an HTML article on iOS, testing with foursquare: <a href="foursquare://venues/40a55d80f964a52020f31ee3">deep link</a>.
Brian