The reason they are mounted perpendicular is to provide diversity in the way your radio sees the incoming radio signal. Because 2.4 Ghz radios have a very short wavelength they are more prone to being shielded or blocked than older radio technology. Items such as the engine, muffler, fuel tank, carbon fiber, or other similar things can temporarily block out the signal to the receivers. If both are oriented in the same direction then when they are shielded is possible that both will not receive signal. By turning them perpendicular to each other you have a better chance of one still receiving signal when the other one is shielded. This is the same reason that the antenna elements in a FHSS radios (Futaba, Airtronics, Hitec, etc....) are placed at 90° to each other as well. It's done to provide your radio with better chances of keeping signal while flying.

Ken