My guess is that the contents of .apk package are extracted somewhere, and the application is registered at some directory so that the application launcher or whatever can f
When you install an app, Android System copies its APK to "/data/app" folder and it named it by the package name followed by the installations number (how many times you install or update the app).
I tried to install an app manually by copying its APK and paste it in the /data/app folder and rebooted my device then it appears as an installed app and works perfectly.
Also I noticed in the link2SD app that any installed app has the folowing:
Apk located in /data/app/package-number.apk
Dex located in /data/dalvik-cache/data@app@package-number.apk@classes.dex
Lib located in /data/data/package/lib
Data located in /data/data/package
Cache located in /data/data/package/cache