Well, we're specifically talking about the Black Books here, but think of all of the quest items you pick up throughout a play-through. Not to mention the still unfixed picking up items before you get the quest, making them permanent items in your inventory (console players).
I certainly agree with all the points you have made and find it irritating that the black books cannot be removed from the inventory. Not sure why it's not possible to put them in a chest or preferably a display cabinet in a house owned by a character. After all, this would not be getting rid of them and it would be nice to see them on display I think.
I'm on my 2nd playthrough of DB at the moment with a new character and was wondering how many black books there actually are, I managed to find 6 on my 1st playthrough but am wondering if there are more to find. Does anybody know the exact amount available?