Several reasons.
- The automatic notification in the GUI only happens every X hours. If you want to install an update sooner than that then installing it manually is the right approach (but I guess you can trigger that in the GUI with more taps if you want).
- The GUI interface for installing (and deinstalling) has been known to exhibit problems, problems that don’t happen when using
apt. - The command line interface gives more explicit control over the exact type of upgrade (regular or full) whereas it may not be obvious which you are getting when using the GUI.
- The name as known in the GUI interface may be different from the package name as used in the command line interface, so if someone refers to an actual package name that you need to install, it may be simpler and more reliable to use the command line interface.