Tolkien always indignantly denied that LOTR was an allegory.
Yes, there are sometimes things to be found in a book of which even the author is unaware. This is particularly true for those writers whose stories sometimes seem to come bubbling up from the subconscious (which is by no means all writers, let me add). We all have monsters from the Id, and sometimes they escape into our stories with us being none the wiser.
I don't, however, believe that anything of the sort happened here, and in this case I am strongly disposed to believe Tolkien. He despised allegory, by the way.