Double teaming can affect a player's FG%, but at the same time, you are leaving someone open which increases the other players' FG%.
The effect of a double team on a particular player depends on the player. For example, a star player who was likely double teamed in real life (e.g. Michael Jordan) may still perform close to his real life numbers even when double teamed. But if you choose not to double team him, he may perform even better than his real life numbers.
On the other hand, a player who was likely not double teamed in real life would probably produce less than his real life numbers if he were double teamed, but probably wouldn't much exceed his real life numbers even if not double teamed.