If you include an MTB wheel freehub design, then I guess there are 3.
But then why not include MTB shifters in this discussion if we are including MTB freehubs? So now we have multiple shifter designs too!
Kidding...kind of.
CT's Huang said Shimano didnt want to do a 10t cog due to drivetrain wear. So based on that, the road set doesnt have 3 different freehub designs.

Shimano is using MTB rotors and 12sp chains moving forward. So they are clearly willing to use MTB gear when they feel its best.