Smashboards

I remember when they made a 3D Samurai Shodown game and cut most of the projectiles only for Haohmaru to get into SoulCalibur years later with his projectiles intact and working perfectly fine

I guess there's probably an argument to be made that 3D fighters tend to just take more of an influence from their predecessors, with Virtua Fighter's greater focus on minute positioning over projectiles and the like directly inspiring other games in the 3D fighter space (like Tekken, DoA, Toshinden, etc) - coupled with the fact that a lot of these games don't have a jump function (so your only option would probably be blocking rather than jumping over them.)

There's nothing really stopping 3D fighters from including projectiles - characters like SoulCalibur's take on Haohmaru or Tekken's take on Akuma, plus (if I remember correctly) DoA5's take on Mai have these kinds of options, but you obviously have to rework balance a little to really lend to their use - it's not as simple as almost every character in the game having at least some kind of ranged option, or at least counterplay.