When is the latest that one may say Al Netilat Yadayim? For instance if one already used the bathroom and washed their hands and ate breakfast, should they still wash?

The "lateness" of the hour is not a determining factor. If you have already washed your hands from the tap and later you remember that you haven't done "Netilat Yadayim" three times on each hand with a cup or other vessel, do it when you remember, but without reciting a bracha (see Shulchan Aruch Orach Chayyim 4 and Mishna Berura there).