I think you're the one who's bought into a joke; namely, secondaries calling his art shit for the past fifteen years without even paying attention.
For one thing, no matter what you think of his early Windows-era art, he has improved greatly. Compare pic related to some of the full-body portraits from Youyoumu: notice how much better he's become at doing arms and legs, hands and feet, and poses.
And you can tell that most of what makes his overall style for Touhou distinct was done on purpose. Compare his early Windows style to his PC-98 style: the latter was a lot more generic, if still fairly blobby and with the same anatomy blindspots. So yeah, since Koumakyou he's kept the same unique, charming style overall, while changing up the details every game to set each one apart, and technically improving quite a bit in the background.
Anyway, you know, all ZUN has ever wanted to do is make music. Making games to put the music in was a skill he reluctantly learned in order to sell it at Comiket, and drawing cute girls was a skill he reluctantly(?) learned in order to make games that fit its aesthetic. So even when his art was kind of bad, I'm inclined to forgive it because it still served its purpose perfectly well.