You know, it’s very likely that Jacob was not the only person to name a kid after Shepard. Just imagine- Shepard saves the entire galaxy, and in the years after ‘Shepard’ becomes one of the most popular names in human history. It becomes expected that at least one kid in every classroom is named Shepard. It’s especially popular among families with connections to the Alliance.
What I’m getting at here is that it’s totally feasible for the protagonist of ME:A to be named Shepard Ryder.