Do I have to repurchase Apple apps through the Mac App Store to get updates there?

Solution 1:

Yes, you do have to re-buy to get updates via the Mac App Store. Via Daring Fireball:

The Mac App Store may show software bought from us previously as “Installed”, even though they’re two different licenses. You will not get Mac App Store auto-updates unless you purchase from the Mac App Store. To re-enable the “Purchase” button in the Mac App Store, just drag the app to the trash. Your preferences/sites will not be affected.

In other words, for apps that use the same bundle ID for the both the Mac App Store and non-App Store versions, the Mac App Store will not install updates to already-installed non-App Store versions, but it will recognize them as being already installed. If you want to get updates via the Mac App Store, you’ll have to re-buy the app through the App Store.

Honestly, I'm really surprised by this.

UPDATE: I'd recommend reading Cabel Sasser's blog post over at Panic about this as it provides a more comprehensive picture of what's going on, and includes some developer-related information.

Solution 2:

Yes. Unless you buy the apps through the App Store, they will not be official App Store apps. Meaning no reinstalling if you ever needed to, no installing on other Macs, etc. And you won't get updates through the App Store, you'll get updates through Software Update (which you can find in System Preferences).

However, if/when you upgrade to Mountain Lion, which came out last week, Software Update has been integrated into the App Store. So all your Apple software, regardless of whether or not it was purchased through the App Store, is updated in one place.

Solution 3:

No, you do not need to repurchase an Apple App through the Mac App Store if you want to be eligible to use the Mac App Store's built-in update mechanism to update it.

You can perform updates of Apple provided Apps which you bought on CD/DVD (before the advent of the App Store) with the App Store's update feature. Even though the App is not shown as Installed normally, this changes to Update if an update is available. This is at least true for me with Aperture.