this is my first response/report, so please be gentle with me.
I am a complete noob in this whole thing and have to do a lot of homework before I can be a worthy member of this comunity, but I am kind of excited on this particular topic.
I noticed the same Herb Node problem in my MaNGOSONE server. I started a Tauren and all along Mulgore and The Barrens there was just one funktional Nod per Herb in both Maps.
But as soon as I started the quest "Root Samples" in Ratchet all herb nods were functional. Up too the Point were I had all the roots together. At this point the Nods were unavailable again. So the Herbs are visible and with the active quest collectable, but as soon as you have your questitems together they aren´t longer...
I have no idea what to do with this information and still trying to understand the database, but maybe it can help one of you. If I find out something else I will report again.