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