GdalTools core plugin "missing metadata file"

I've resolved this by learning from Michael Stuyts' experiences in his comment above.

After upgrading from QGIS 2.18 to 3.0, I also had an empty folder "C:\OSGeo4W64\apps\qgis\python\plugins\GdalTools\tools". I removed the GdalTools folder and this has made the error disappear from the "Manage and Install Plugins" window.

You shouldn't need the GdalTools plugin in 3.0 -- it was removed and the plugin's functionality was merged into the processing plugin.

If you go to Settings -> User Profiles -> Open active profile folder, what do you see listed under python/plugins?