Samba is a networking protocol so that Linux can communicate with Windows, and do file transfers, etc. I don't think that it has any inherent ability to "hide" files... that is more of a filesystem and/or permission capability, and each operating system hides files differently.
See this for more details about how Windows/Linux/Mac each do it their own way.
So, basically, I don't think it is possible to use Samba to copy a file that is hidden with Linux (a dot-file or dot-folder) to a Windows partition and have it
automatically be hidden in Windows too. However, after you copy a Linux dot-file/folder to Windows, you can then change the attributes of the file/folder so that it will also be hidden in Windows. You will have to manually do this, or create a batch file to help automate the process. See
this and
this for a little more information.
Perhaps a BASH script from Linux could be used more effectively than a batch file from Windows, but that goes well beyond my skills.


Cheers