Why should HTC change the damage model for two planes that are almost (apart from shorter wings) identical?
Yak3 Dimensions:
Span 9.2m
Length 8.55m
Height 2.3m (inc landing gear)
Wings area 14.4m^2
Yak9u Dimensions:
Span 9.74m
Length 8.55m
Height 3m (inc landing gear)
Wings area 17.2m^2
The only answer I can think of with the Yak 3's ability to take punishment is a combination of it being small to start with, and being assigned a higher than usual amount of hit zones for the damage model. This would make it more likely that damage received would be spread over several hit zones, and less likely to accumulate hit points to a point of failure.
In that type of damage model any aircraft with a more diverse array of critical components, for example 3 smaller fuel tanks in each wing instead of 1 large one would benefit. Of course this is me merely speculating as the only person who would know for sure would be whoever modeled it.
In my experience, I don't think it as an unfair comment to say the Yak 3 and other planes in game are overly tough.