I believe you're confusing the .DS_Store files which are per-directory and used for storing Finder window metadata with the "._" prefixed files (so-called AppleDouble format) which are used to store a file's resource fork. (These also show up in zip files created via the Finder.)
You can configure Samba to store resource forks using xattrs instead. See fruit:resource:
https://www.samba.org/samba/docs/current/man-html/vfs_fruit....
You can veto the .DS_Store files. The consequence to Mac users is that the Finder won't remember any display changes they make to windows that correspond to network folders.
https://www.samba.org/samba/docs/current/man-html/smb.conf.5...