This is a vast and excellent game by a small company.
They took a few shortcuts, and I'm not inclined to be harsh.

Needing to have a book in inventory to read it is a pain, sure.
That isn't likely to change because of the way quest events trigger.

To make it less annoying:
  • Aside from Craft books:
    • Read everything you find.
    • Then stick it in a backpack on your main character and forget about it.
    • If you need it to do something later, the script will find it.
    • It won't clutter your inventory.
  • For Craft books:
    • The Journal lists what you've read, by title, under "Recipes".
    • If you don't open the list entries it's a very quick scan.
    • When you find a Craft book:
      • Read it, then drop or destroy it.
      • You won't need the money after you loot Cyseal.
      • If you're an uber-role-player, you're on your own.
        I never have the mental stamina to carry that through.
    • For a quick check in a trade session:
      • Close the trade.
      • Open the journal.
      • Open Recipes and scan the list.
      • Now you know if you've read it.