MS Graph will provision a drive resource for each OneDrive SharePoint or SharePoint document libraries associated with teams.
Using this, you can search each drive on its own using its id like by calling GET /drives/drive-id/root/search(q='search-text')
You can get the users drive-id using GET /me/drives
Or teams document library drive-id using GET /groups/{team-id}/drives
Or just get GET /drives
depending on your scenario and permissions.
So the base line is if you are using the drive-id, you should be able to search each accessible drive on its own. Graph Search Files Docs details this further.