Yes I think you could the “true” list of used versions (and apps) with something like
grep -nr "nodejs_version:" /etc/yunohost/apps/*/settings.yml
And then you could remove unused versions
Note that sometimes you may see for example version “14” or “12”, and this should in fact correspond to something like /opt/node_n/n/versions/node/14 which should be a symlink to the latests 14.x.y version … But other versions (not pointed by a symlink) should be removable