So, I have a number of the witcher school treasure hunt maps. Even though I have read them, they don't get moved to the non-quest item category. I also know that I am missing some armor/weapons from my diagram list, but I still don't have a quest marker for them.

Bug? Working as intended? Am I doing something wrong?

When you read a map it should open up a new quest in the Treasure Quests section of the quest log and remain there until you find everything, then the quest should mark completed as per other quests. I've noticed that the game keeps things in the Quest item section of the inventory though sporadically after quests are completed. Some quests finish and the letters/items stay in the quest item inventory, some items move from quest item inventory to one of the regular inventory areas, and some items seem to just disappear when the quest is complete, while others you can lug around and use such as the green ghost lantern and the magic illusion dispel disk thingie for example.

If you've completed a treasure hunt quest and the map sticks around I'd say it's either intentional or a bug. I can't see any value in the game leaving "crap" in the inventory when it no longer serves any purpose in the game, the inventory slots are already tripping over themselves in abundance.

I wish there was a way to flag books as "I read this with my human eyes and there's no way you can determine that algorithmically" that has to be manually toggled, so that when we obtain books/letters etc. they have an icon showing "unread", and merely viewing it does NOT set it to "read" because you can view something either purposefully or by accidental mouse click and choose not to read it right then, but if you don't - you have no idea what in your inventory you read already or not. Skyrim was TERRIBLE for that because it has like 238429347 books. I end up keeping a text file on a 2nd monitor and whenever I read a book I type out the title and keep track in alphabetical order. Then I can sell the crap read books to declutter.

I wish we could do the same with maps and other fluff.

The solution is very simple and it was implemented in Witcher 1. It was very clear which books were read and which weren't. Yesterday I've stumbled upon a guy in Novigrad who sells only books (lots of them). I knew I've read some of them but 'thanks' to the great game design I didn't know which ones. It's the same mess they did in Witcher 2 and still they didn't learn anything.

Shamefur dispray!

You don't understand me. I was refering to the fact that when you buy/find a lot of books, read them and finally sell them you don't see them as already read when you stumble upon a book seller that sell only books (the guy in Novigrad). I don't write down the names of all the books I've found/bought. Why should I? The books/maps that I've already read should be crossed out or sth similar. So I wouldn't buy them again.

Not really. Some new items go to the top of the inventory screen, and some to the bottom. On top of that, if its gone to the top of the screen then it won't have that asertisk next to it because you start out on that item when you open the screen. Also, if you browse your inventory first without reading that book, you are screwed.