In what Folder are Dock Applications are stored?

The "links" to the apps are stored in the file ~/Library/Preferences/com.apple.dock.plist in the key persistent-apps with ~ being the "shortcut" to /Users/yourusername:

In the example above I expanded the entries for App Store and Launchpad. The only exception is the Finder.app. Probably it's a fixed entry "injected" by Dock.app itself.

Normally, each user has its own com.apple.dock.plist file.

The apps you see in the Dock are displayed programmatically from data stored in a property list (.plist) at this path:

/Users/<your_user_name>/Library/Preferences/com.apple.Dock.plist

There is no folder of 'shortcuts'.