If a *specific* anchor may be externally referenced, There is no way to know what another manual might reference. A new reference might be made at any moment. Therefore the only reliable thing to do is take care of everything at the time of creation.
Granted the extra files are ugly, but ... harmless. If they bother you enough, don't generate them and wait for people to complain and handle the complaints. I agree the chances of an external reference to any given anchor (or node for that matter) are very small ... but nonzero. k
