With the exception of the user content folder that will automatically be re-scanned, upon opening of Cubase, and checked even if you have purposely UN-checked it, any folder can be either checked or un-checked and it will stay that way…permanently. Therefore unchecked means media bay won’t “see” it. Leaving things unchecked as advantages for preset organization and loading presets, but that seems to be a lost cause.
Unless I’m mistaking you, sure you can optimize media bay. A few minutes reading the basics about media bay in the pdf should answer these questions.
If you are referring to the exception…the user content folder, it will always be re-checked. I have asked for reasons, and the only guess is sort of for preventative measures or dumbing down a powerful feature.
There is also a way to click any file and media bay will show you were it is in Windows Explorer, if that is what you mean?