I think aircraft that were designed **and used** for a specific role should be classified as such. If the plane didn't have hard points for ordnance and the units in which they flew in did not partake in ground operations (moving dirt), then shouldn't they be classified as "fighters"?
There are few aircraft that are truly absolute (in terms of AH fighter, attack, or bomber classification). The B29 is one of them (bomber). The Ta152 and Me163 are another (fighter). The IL-2 is yet another (attack, i.e.: direct fire support). Aircraft like the Spit 16 were meant to be used as a direct fire support ground attack plane (gasp!), yet it derived from one of the best dog fighters in WWII.
As the war went on more and more planes were used to attack ground targets because the Axis had fewer and fewer planes.
I don't know why HTC classified the Yak-3 as a combo plane, but that is their prerogative. I think having the Spit 1,5, and 9 as fighter and the Spit 8 and 16 and fighter/attack is proper though. I'm not up enough on the different Yaks to comment historically speaking, but I'd be willing to bet that the Yak-9U was used more exclusively for fighter duty over the Yak-3 simply because there were more Luftwaffe planes to combat when the Yak-9x's were in the air vs when the Yak-3 was in the air, figuratively anyways. Just a guess.
Also... just because a player can up a Yak-x and kill a gv does not make it a combo plane. Just because a tank uses the main gun to bring down a plane does not make it an AA platform.