This is an issue no matter what once the app is updated through the market. You can put it in /data/app/ if you wanted and it would still be the same thing. Even if you put it in data, some things will not be able to be updated via the market without removing them first since we change the signatures in order to theme (Facebook and Twitter are great examples). Apk's that don't have their signature broken, can still be updated, for example, I have YouTube in my /system/app themed but am still able to update since I didn't decompile or recompile it.The update will override the themed version of these apps even if they were in /data/app. Google has decided to make the traditionally "system apps" released to the market, allowing them to provide updates, but complicating things from the themeing perspective. With every update, we need the new copy to retheme the apk.