I don't think you can get updates through the app store unless you purchased/downloaded through the app store in the first place (so you don't need to worry about these features suddenly dissapearing from your software.) As others have pointed out, if the app store was able to update non-app store purchases, then that could lead to Apple updating pirated software.

" don't think you can get updates through the app store unless you purchased/downloaded through the app store"
That's what happened to me! TextWrangler was installed before (downloaded from the developer site) and the App Store proposed the update....

Really? It never tried to update mine... And I wouldn't think Apple would be allowed to update software that they didn't sell you...