I have noticed CFD can make the weathervaning worse, I think for the exact reasons you said. Lack of contact point friction and complexity seem to be the culprits with this issue.
On a different note, I have noticed a few aircraft (Asobo and 3rd party) where geometry of the tail surfaces is wrong. A lot of developers seem to think that htail and vtail areas should include the control surface area as well (rudder and elevators). The SDK guide clearly states the opposite, but I still see vtail and htail areas that are double or more what they should be. Imagine the weathervaning effect of having a vertical stabilizer twice as big as it should be. The stock B58 specifies a vertical stabilizer area of 25 sq.ft. when in reality it is less than half that.