Ok - so investigation shows that themes etc. appear to be managed by soft-links in the folder linked as ‘current’ which all appeared to be pointing to the right place… however, despite stopping and restarting ghost, the old version was persisting.
I removed the casper link - which looked like it was pointing to the correct place, recreated the link, restarted ghost - had a permission warning, fixed the permissions and hoorah - Casper is now a shiny 3.0.2.
My conclusion is that there was a permission problem or customisation with this blog, that has now been fixed. Probably because this host runs multiple blogs and all the ghost versions are installed in /usr/share/ghost/3.0.2 etc - it seems that some of the permission checks were being skipped because of the soft-links.