so it sounds, to me, like this was a problem that came up in the past, and was abused.
A mixed league that stacked themselves using subs that made them an all-male team.
A league can be handicap AND money (we're in one now) and any league that has competitors in it can be very competitive, so rules help give everyone a sandbox in which to play.
To me, VACANT is gender-neutral (meaning neither) - it should not be considered for anything, and in fact should be penalized so as to encourage a team (or league) to find someone to fill it. It should definitely not be considered male or female to fit the legal lineup requirement. If so, this would enable an all-male team to be legal with one vacancy. That's not fair to the rest of a mixed league (when "mixed" is required).
And I don't think the subs make that much of a difference - as long as the minimum requirement is there. This means that if the solo lady has to be absent, then a female sub is required. If one of the guys is absent, either male or female sub would work. If both of the guys are absent, at least one male sub would be required.
I'm not hugely in favor of forced mixed leagues - I'm more in favor of a maximum entering team average as this encourages high average bowlers to get lower average bowlers to join them.