You might need to log a ticket in game with the support team, who should hopefully be able to track the item and find out what happened to it.  I assume you aren't too worried about the rare book itself as you have 100, but are more worried about other more valuable rewards that are being lost

I will contact support.  I want to be sure the lego book I get from hero does not vanish.  

I think I found part of my answer.  I had 100 rare books.  I used 15 and then 12.  I now have 90 rare books.  The books are there but not fully displayed in my tavern.  

Is there any way to find out exactly how many hidden books that I have?

I've...never heard of this before. Like Rose has said, your best bet is contacting support. As far as I've known there's no limits to books though if there were one, I'd guess it's 999.