Probably a stupid question, but I would like to clear up any doubts... For a native speaker, is there a difference between the word お祖父さん and the word 祖父さん? The first one, simply, is more honorific?
Yes, おじいさん is "relatively" more respectful. But it's better to regard おじいさん as 'plain/neutral' and じいさん as 'usually rude'. You may address an old stranger with おじいさん, but you must not use じいさん unless you really want to be rude. The same is true for おばあさん vs. ばあさん. Some native speakers refer to their own grandpa/grandma as じいさん/ばあさん in the most casual settings, but I would say there is almost no reason for a nonnative speaker to ever use じいさん/ばあさん. (There are even ruder derogatory term, じじい and ばばあ, which you may see on dirty net forums)
By the way, 祖父さん【じいさん】 is a relatively rare ateji. It's pefectly fine to write this with all-hiragana.