Not official lore, just throwing ideas that I've seen before, and conjecture that I haven't:
imporation of men is very selective, and population control? Deals made to keep Gensokyo like a hunting preserve, with human preservation involved for workforce to produce amenities. Because fairies tend to be too scatterbrained to do any difficult "thinky" jobs. Maid work in the SDM is ok.
For complex work, rely on humans run a tight ship under Keine, who can just retroactively erase anyone who goes missing, or anti-union "scabs". Or deal with Kappa, who are now kinda under the "protection" of Suwako, Kanako, and Luigi Reimu. Kappa allied with Tengu, because they'd rather hate each other as allies, than be driven underfoot by newcomers, and all want goddesses on their side because they're sick of being fucked with by Onis.
Justified paranoia and insular groups, because Gensokyo is full of nonliteral assholes. Reimu's generation is innovating Danmaku play. She needs to be the baddest mofo out there to force everyone to play nice. Even then, she's just one girl, who can't change everyone's minds right away.
Nobody wants into mutually assured destruction with bullshit abilities that exist in Gensokyo. So it's Game of
Thrones Touhous.
Some goddesses are native. Others slip the net. And the smart ones bide their time, or seize a good opportunity before they establish themselves, typically through incidents.
Most existing men were taken to Makai? Low fertility rates, tradition, and handselected genealogy births mostly women, in addition to the iron-fist control of human population? Maybe Yukari found a border that turns off male-birth, and Keine missed her timeframe to reverse something that isn't easily noticeable. Or Keine would rather have it, as a mixed blessing.
More jokingly, Yukari wants to keep the ecocknomy under wraps. Wealth hoarding.
If you got inserted into that setting as a magical being, would there be any reason why you wouldn't be a dude?
One dude can many many babies from a group of women, and it might "short circuit" an anti-male birth curse or border manipulation. Being magical on top of being a dude, like winning the lottery, then being dictated on how you must spend it. They're "recruited" by the state. They can't have freedom.
Sex is nice, but you'd be like a bird in a gilded cage. Their semen is a controlled substance, because it getting into many women could be the start of new empires, dynasties that give the powers that be, a headache. Like if some magical humans escape into the mountains, it probably won't be in tengu land. Then they go Sinjid Shadow of the Warrior, and send powerful assassins at enemies. Might be why the Mikos were all but wiped out by youkai. But then Reimu was the only one left to take from her divinity's power, making her
The One, and became really hard to kill.
Green Reimu doesn't have that power despite being a miko too. She's using an offshoot of Kanako's and Suwako's.
Marisa is an exception, having liscenced parents, and she found a legal loophole in magic studies, because she didn't go for being a youkai hermit, and is a useful mercenary. Alice has diplomatic immunity as a dual-citizen of Makai, so long as she does not start distributing her power to residents abroad.
I can go all day making up bs.