Version 22.00 of Baseball Mogul 2019 (released on March 21st) includes about 60% of the "Top-10" prospects for each team. The other 40% were omitted were several reasons. One is that I was using "Top-100" prospect lists, which is only about 3 players per organization. Another is that I can't yet include players without any playing time in either the major or minor leagues (e.g. Victor Victor Mesa and Marco Luciano).
Thanks to some help from Mogul fan Damian Henning, Version 22.02 should include about 15 more "Top-10" prospects, leaving less than 3% of this group missing from the database.