Can some folders be hidden from Available Data Extensions or Target Data Extensions?

Yes. If you want to only see Data Extensions from certain folders in the Available Data Extensions section, this can be set up by DESelect support. Similarly, you can decide which folders are available in the Target Definitions section in DESelect.

You can choose if you want to show only the listed folders or if you want to hide only the listed folders.

Please get in touch with support for more information.