Is there an indicator for already read books?

IF you only care about the skill books, then you can safely sell all the books under a base value of 30 (it may even be 50, but 30 is definitely safe).

Then you only have to open each one of that value or higher. There are only 90 different ones in the whole game (five per skill) so that shouldn't take too long as I assume you only have a small fraction of those.

No such thing exists in the standard version of Skyrim, but I found this mod that marks books as read!

https://www.nexusmods.com/skyrim/mods/20910

For the books you've got stashed away somewhere already, you are sort of doomed, other than referencing a list or using the guidelines w/r/t book value. However, you should be able to rip through them all fairly quickly by repeating the key sequence 'E/Tab/S' (on the PC, anyway) in the appropriate inventory section, since you only need to open the book to get credit for reading it.

In the future, you can read books directly from the looting interface by holding the Shift key (again: on the PC, of course) and interacting with the book while it's still in the container being looted. Incidentally, the Shift key will also allow you to equip items directly from the looted container/body area of the looting interface, so that you need not take the item first and then move to your own inventory to equip it.

And you don't have to be insane; some of the books are actually fairly interesting, and help to flesh out the world a bit. It is true that the reading experience itself leaves much to be desired, which is why someone make all the books into a single Kindle .mobi file for download.