You can set how the names will be pronounced, in addition to how they are spelled, when editing a player.
In most cases they have all the names programmed into the game, even if they don't have the minor-leaguers in the game (when a prospect isn't in the game its due to SCEA not having the rights to their likeness, this means SCEA can't put them in the game until they are a part of the MLBPA, this doesn't mean their name is not something they can program into the game for players to use when they create them).