The icon name and folder name have not changed after the updates

No impact and common Eclipse update behavior here.

You've perfomed an update ... means kind of patch of an existing material. Such is fully functional and no drawbacks.

If expecting new folder, new icon you have to perform a brand new fresh install from an installer. Installers are available on www.st.com but as 1.3.1 is minor release not sure such installer is delivered.