I've heard that bookshelves eat books, deleting them from the game. Does that happen often? Should I put my books in a barrel or something until they get patched?

They do 0.0

I haven't seen this happen yet, I sure would hate to lose my dragonborn book.

I've had problems like this in the markarth house

yeah I had that issue as well, and even when the book completely disappears, you can't put another book in the missing slot, it is permanently gone as well as the book is gone. but after the patch now you can't even interact with the shelves, so you can't retrieve any of the books you put down as well as place any books on. if you are still playing before the patch, I noticed that if you spend too much time in the house doing other things, then it was more likely to swallow your books after you put them down, but if you go straight to the shelves, then it would go by fine, but don't ever save your game manually inside your house, on several occasions doing so would make the shelves in my house disappear and not come back

I've had that issue, so every time I go to rearrange my books I save first, then open a shelf. If it says anything other than "you have 0 slots left" then I know it ate one. If it DID eat one, I revert to said save, then go to the offending shelf and manually take each book off.

See, all the books are there physically, just not listed in the shelf's inventory.

Also on some occasions loading a save inside the house results in bookshelves, tables, etc disappearing. Reloading again seems to solve that problem, at least for me.

I see that the 1.2 patch broke bookshelves as well. Since my last character got denied the main quest due to a bug, I was going to use the Oghma Infinium bookshelf glitch on my new character and had already deleted my old save file. With my luck, by the time they patch the bookshelves to get them working again, they'll patch the Oghma Infinium glitch as well...

This was another problem I didn't have until the 1.2 patch

I have the same problem. My bookshelves in my house at Solitude no longer work. Some of them the books disappeared, some the books stayed. Either way, I can no longer interact with some of them. Some shelves still work, but I'm afraid to mess them in fear they will stop working too. Lost some good books, hopefully they'll correct this soon.

No they are not. If you have this problem and have lost books, what you should do is revert back to the autosave from entering the house before losing your books, then just drop all books in your inventory on your table in your house, then DO NOT TOUCH the bookcase until it is reported as fixed. That's what I'm doing.