Don’t change the database entries. To achieve a single database between local attached and remote clients use path substitution (see below) .
Alternatively you can use Kernel Mounts on all and mount the disks/shares on all of them on the same folders.
While you may even get away with the extra loop going through Samba as you do now it is surely extra burden.
If you would like to use a MySQL database for several Kodi clients that use different methods to access the shared media (e.g. a mix of SMB, NFS and/or system mount based access), or have need of modifying a path of an existing source (such as converting from a Kodi path to a system mount) you can use the path substitution function of Kodi to facilitate this. The following guide will provide instruction on how this works, including a section specific to MySQL usage and how your sources should be configured.
Please see [HowTo] Repairing File Paths with Path Substitution for details.