The problem with documenting those ($nopnick, $nhnick, $nvnick) is that they are deprecated, and could be removed at any time. There is not much reason to document things that are being replaced, and doing so practically encourages people to use them ("but, it was in the help file last version, and now it suddenly doesn't work?!?!"). I do think that some things missing from the help file should be added, though, such as $nickmode, unless that too is deprecated. I'd also like to see the me: event prefix in the help file, as that is one that I find to be extremely useful, though a bit confusing when trying to explain to people that it's not a userlevel
edit: on the other hand, I can't think of a single thing that has actually been removed since it was deprecated. They always seem to just get hidden. Am I mistaken?