/usr/libexec/makewhatis used to fix this until Apple forced the man directories read-only.
Some commands are available on install, others get installed with certain new features/options.
Even apples updates do not rebuild the apropos database properly because it should be in a writable area.
unfortunately makewhatis, which is whats behind apropos, uses a different algorithm than MAN does to list pages
if you do
apropos ncdestroy
you should get
ncdestroy: nothing appropriate
yet
man ncdestroy
does yield a page (at least here it does)
this seems to be a result of MAN actually using both the MANPATH and PATH as well as some other heuristics to locate man pages
Its described in the man page for man under SEARCH PATH FOR MANUAL PAGES