I doubt there has been any official confirmation, but I do see several possibile contributing factors.
Dark types are used by the nefarious Teams
- Generation I: In this generation, there are no Dark-type Pokémon. The antagonist Team is Team Rocket. Their members often possess Poison-type Pokémon
- Generation II: The antagonist Team is still Team Rocket. Their lineup now consists nearly entirely of Poison types such as Arbok, Zubat, and Vileplume, but, crucially, with the addition of the Dark types Houndour, Houndoom, and Murkrow.
- Generation III: The antagonist Teams are Team Aqua and Team Magma. Of course, their main themes are water and fire, respectively. But they employ dual-types such as Carvanha, and Sharpedo, along the pure Dark type Mightyena and a few Poison-types.
- Generation IV: Team Galactic are the antagonists. We have Stunky, Murkrow, Honchkrow, Sneasel, and Weavile.
- Generation V: By now it should not surprise us to see Purrloin, Sandile and its evolutions, and Scraggy and its evolutions as regular players on Team Plasma.
- Generation VI: Team Flare is the enemy here. They use Houndour, Houndoom, Mightyena, Purrloins and Liepards, Scraggys and Scraftys, and Murkrows and Honchkrows.
Dark types, then, are the most consistent marker of the villainous Teams. It is true that Normal-type Pokémon are often used by Team Grunts, and that Poison-types often show up as well. But the choice to have Poison-type gym leaders was made from the very first generation, with Koga. Too late to back out now.
I suspect that The Pokémon Company's designers fear theme dilution. Dark types are the marker of shady criminals. If they are associated too heavily with themed gyms, their status as markers of ill intent could diminish.
Perhaps related to this, there is the following....
Dark Pokémon are evil (or at least あくタイプ).
From what I understand, the name for Dark types in Japanese is あくタイプ. The part あく seems to translate to "evil," or even "scum," while タイプ means "type." Surely evil, "scum" type Pokémon are best associated with villainous types, which most of the gym leaders really are not. Sure, some of them may cause people to pass out at their concerts from intoxication, but on the whole they aren't into world domination. That is the province of the Teams. And thus Dark-types are a better fit for Teams than gym leaders.
Of course, many Dark Pokémon are not truly villainous, and some are actually quite nice. Darkrai, for example, held Palkia and Dialga in check.