Installing System Shock 2 onto Batocera has proved to be tricky. The eventual solution I found these posts here:
https://www.systemshock.org/index.php?topic=106.0
https://www.systemshock.org/index.php?topic=4141.0
It turns out that all that is needed is the content of the Sshock2 directory. Put that on a standard Windows PC – not a WINE instance at this stage.
The get and run ss2tool on this directory – I tried in WINE, but the RSYNC that it needs to run would not work for some reason.
Finally, copy the Sshock2 directory into a WINE location. This should be made using the command line as shown in WINE in Batocera.
Everything should now work.