I haven't had a reason to pull my Baseball Encyclopedia off the shelf in a while (and, yes, I'm coughing from the dust), but I looked Keeler up and they didn't have any strikeouts listed for most of his career, right up to 1910. I don't know when enough data came in for Baseball-Reference to start putting some K totals with batters of that era, but chances are high that they represent some verified data but nowhere near all of it. Just as they have populated Negro Leagues stats with what they do have rather than waiting for a full season's boxes to materialize, I'd imagine they are using what they have.
None of this explains where the sim got its stats from, of course.