The encyclopedia is generated from whatever items exist and Vicky just has them because she's always had them.
I think I've seen mention of just having the item being enough ... maybe that was just a plan though.
I'm not super certain that's true for non-essence consumables: I still had to do things like equip a rose in my own hair, smell a bouquet of roses, and hug a teddy bear to add those items to my encyclopedia, but I've never fought an alligator in any playthrough and already have their essence in the list. Similarly, I already own chocolates and some miscellaneous races' transformative items, but since I haven't eaten any so they're not yet in there.
I might be locked out of adding the reforge hammer to my list because I decided to learn earth spells before using one, and apparently that school of magic nets you free dye/reforge functionality. Whoops. I guess I could just start a new game and 'speedrun' it, or edit the properties.xml file that seems to track that info to get it.
Consumables aside, it
does look like weapons and clothing are added to the lists when they've been in your inventory, but a separate "encyclopedia entry added" message still triggers when you've equipped them. Which is a bit strange if that's really how it's working right now.
Thanks for clarifying my other two doubts, by the way. Much appreciated.
Edit: I'm enchanting a tattoo and apparently the capacity cost for Fertility 'to add' doesn't properly update (displays as 0 before adding any of the boosts, but adds 1, 2, or 3 to the total cost when added to the 100 enchantment slots- it also subtracts from them if you add a drain, though... which means you can cheat the capacity limit system by making yourself extremely unfertile or unvirile - I note that virility never adds any capacity cost the way fertility does, though). So that's something to probably report as a bug unless it's intended.