I think we can now consider /var/run fully deprecated and everyone has moved on to /run. Even Debian, who are normally very conservative, jumped on early with this transition, even before they adopted systemd. So we should update everything in ThinLinc to use /run instead of /var/run so we don't rely on compatibility behaviours.
We don't know of any practical changes of doing this at the moment. But we rely on the fact that /var/run is a symlink to /run at the moment. That symlink could in theory be removed in the future.