Here's the information we have on "Saburo" and tsuushou in general.
The short answer is that it was common for members of the buke or warrior class to have a tsuushou and a nanori. Since SCA members are considered to be minor nobility by default, it makes sense for you to have a tsuushou. Saburou was one of the most common tsuushou in Japan, and it would be completely appropriate.
The long answer is that "Saburou" does mean literally "third son" but it doesn't necessarily mean that you were the third son of the family. Many tsuushou had implications of rank--the element "rou" was derived from a Chinese noble title and other common endings of tsuushou (such as "-maru," "-notsuke", and "-emon") also originated from titles. In fact, some "middle names" actually are titles; these names are called "ritsuryou."
You mentioned that you were thinking of using "Hidenaga" instead of "Nobumaru" as a nanori, and we would definitely encourage this. Your full name would be Akechi Saburou Hidenaga, which is a completely appropriate name for medieval Japan.
Solveig Throndarsdottir researched this letter.
We hope that this has been helpful, and that we can continue to assist you.
Academy of S. Gabriel