Basically, as a best practice, we should tell WYSIWYG modules to look at filter_form and/or check using JS to see if an input form selector is available, and only then replace with a rich text area.
I ended up with something like that when I couldn't find a way to control which fields the TinyMCE module should pimp. I made a small custom module used filter_form() to give my chosen textareas the class of mceEditor, and used hook_menu(!$may_cache) to load TinyMCE and instruct it to only pimp textareas with the mceEditor class. I've been thinking whether to contact the devs of TinyMCE module about this, should I still or are they already on it?
And yes, a "real" hook for D6 would be even better, although I get the sense many folks are against WYSIWYG in general, but I'd rather not get into a religious war....
It would make it easier, and I think it would promote better implementation of WYSIWYG editors, although filter_form() and hook_menu(!$may_cache) JavaScript will do it.