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?
As I can remember, Google first packaged their apps as system apps. But from 2.1 (I can not remember exactly) they started to put them as ordinary apps. And in their words, explanation was something like "we want to update our apps more frequent, so you can download updates from Android market and don`t have to wait for new Android system version that have packaged new system apps in it". Also I read some post from ROM developer that they put some app in system/app (system app folder) and that it did not behaved as you want (uploaded app on market with greater version did not updated their system app and behaved like a different app in respect to installing it). Some others report that when they install market version of the app, android deletes their system app with same package name and leaves just that app version from market installed as ordinary app. So, I would say you can not get desired behaviour.
According to the approved answer the system apps cannot be shown in MyApp and be updated.
Maybe this questions was asked and answered too long ago, but according to Google developers site though, it looks like the system apps should appear in MyApps and could be updated.
The user’s system apps (including any pre-loaded apps) are shown in the My Apps section of the user's device in the Google Play store as soon as an application with the same package name is uploaded to the Google Play Developer Console, even if the application is unpublished.
according to the same page, Google Play can manage updates to preloaded applications, provided the following conditions are met:
The preloaded app needs to be in the system partition
The preloaded app needs to be free
The preloaded app needs to be signed with the same signature as the app published in Google Play
The Package Name of the preloaded and updated app needs to be the same
The Version Code of the updated app needs to be greater than that of the preloaded app