I don't know. Only id can answer that. But I doubt they thought this hard about it. But the Quad and the BFG and the big bonus power items ARE in Quake 3. You can either move to a no-items arena such as Rocket Arena 3, or you can learn to abuse the exploit of item running yourself.
Item running IS part of the game.
Play what you like. Just don't call yourself l33t because you grab more pickups than other people. As usual, I disagree with PainBerry. He and I have a long history of disagreements but they're usually fun and well worth having. I hardly feel that things freely available to two parties make things unfair.