How does updates notices appear on Amazon EC2?
Your EC2 instance is just a machine like any others in this respect. Your package management updates the package lists from the repositories regularly by default on Ubuntu. When you log in to the system a script queries the package management for the amount of updates in the regular and security channels and displays it.
If these updates are new how are they shipped from Canonical to Amazon Server?
Canonical publishes the packages in the main repositories and also sets up mirrors to which your machine connects to in the default install. See the file
/etc/apt/sources.list and files in
/etc/apt/sources.list.d/ (if any).
Around the globe, many mirrors exist and Amazon is just one of them.