It's been a day of head scratching but it looks like I've gotten to the bottom of it.
I trashed prefs a few time, each time the ports would show up the first time I launched Logic and disappear the next time I launched Logic.
I had a lovely episode of the Digi Core Audio Driver crashing Logic on launch consistently. Incidentally for THAT problem this doc helped:
http://avid.custkb.com/avid/app/selfservice/search.jsp?DocId=211059&NewLang=en
Anyway, after I launched Logic the last time, the MIDI ports were not there in the "click and ports" layer of the environment, as discussed. I happen to hit my A-80 MIDI keyboard in frustration, sending a MIDI signal through Logic. Suddenly all the ports appear, as if I woke it up!!!
In conclusion, if your MIDI setup does not show up in the "click and ports" layer of the environment window, hit your MIDI keyboard to wake it up.