Not sure that will be possible. Since you can't actually delete those applications from the system, I don't think you can modify their Finder attributes, which would be the only way I can think of to hide them. Meaning you would do something like:
chflags hidden /Applications/App Store.app
You could try the above, but I have a feeling the OS won't allow you to make such a modification to protected applications. Most, if not all of the apps that ship with the OS these days are protected. Even things like Chess.app which is totally ridiculous, but that's how it is.
If you run the following command, you will see all the Apple apps have an extended attribute called "com.apple.rootless" on them, which means they are protected even from root.
ls -l@ /Applications/