My experience has been that the game does use flight distance as the tiebreaker at equal hop count. For example, going from A to D, with B or C as the intermediate option, the game will always pick the one with the A and D wormholes closest together. And of course about half the time that's not what the player wants, if one is an empty fully-neutered system and the other is a mostly unneutered home of the threatfleet...
This is only for the game's logic for routing player fleets over multiple hops, but presumably the AI uses the same logic for itself.
