I'm not too big on competitive and I'm unfamiliar with doubles, but I'm 89% sure female Indeedee is more common in doubles because it has a more supportive movepool and different stats compared to male Indeedee that allows it to have more relevance in the doubles scene. Some gender form Pokemon, especially from the more modern gens, have learn pool or stat changes that make them different from their counterpart aside from a visual change, and in the competitive scene, movepools and stats are the reason those Pokemon are picked over the other form, not because the players simply like one gender better.
Although there are some abilities that have gender based effects and I'm sure some people have used gender mechanics to their advantage before (I remember seeing a short about how using Female Greninja was a disadvantage in Gen 7 because it revealed you weren't Ash-Greninja, which can only be male), the majority of the time, a Pokemon is going to be competitively viable and more common because it is good stats/typing/moves wise, not because it is a specific gender.
Basically, if there's more of 100% male Pokemon used, that's likely because the Pokemon themselves are great in battle and happen to be locked to a specific gender. As for most normal gender ratio Pokemon, outside of probably a few select examples, a gender might be more common out of randomness or player preference for their teams.
