I've updated VB3-II to version 2.0.0 but Logic can't load it

You probably had the old version installed. You should uninstall the old version first. To do so, you have to remove the files:

/Library/Audio/Plug-ins/Components/VB3-II.component
/Library/Audio/Plug-ins/VST/VB3-II.vst
/Library/Audio/Plug-ins/VST3/VB3-II.vst3

If these files can't be found in the system library, try searching in the User library. User library is hidden by default, but you can open it from the menu Finder -> GO -> press the "option" key (ALT) on your keyboard, and the Library will appear in the GO menu.

Also remove the Standalone app from the Applications folder.

Finally, install the new version and let Logic re-scan all new plugins.