First i've asked this question: Can a system app be updated?
I did a little experiment that managed to confirm that answer:
Just added an app to the /system/app with same package, keystore and lower version on manifest and and after reboot i see the app on drawer (the app is indeed installed - i manage to do this with a rooted phone).
But now the market doesn't show the app on the My Apps list... but when i search for it on the market, it appears as installed and having a update.
The update can be done there (as answered here Can a system app be updated?) without a problem.
The real question is Why doesn't the market show the installed app on "My Apps"? It's because it wasn't installed from the market itself? But why then do Google Maps appear?
It's just a matter of time? Or do i have to do something for the market to recognise it?