The crop duster scene makes no real logical sense: having lured him to a secluded area to meet with a nonexistent person, why would the bad guys try to kill him in this fashion instead of having one of their people he hasn't seen yet walk up to him and then shoot him?
Alfred Hitchcock was fully aware of this during filming, but correctly predicted that the audience would be so invested in the film by that point that they wouldn't stop to think until after it had ended.
Hitchcock is, after all, the one who first spelled out the icebox moment.
I always assumed they wanted to make it look like an accident. If Cary Grant was found with a bullet in him, the police would start questioning the last people he spoke to, and their cover could be blown. Whereas if he got killed by a low-flying crop duster....
The cropduster scene also makes no sense on another level: wouldn't the bad guys ask themselves why Roger Thornhill is traveling to the middle of nowhere to meet George Kaplan (at a rendezvous he thinks Kaplan arranged) if he really is George Kaplan himself?
Eve knows that Thornhill is Thornhill, and she knows that Kaplan doesn't exist and is a red herring, but she has to make sure Thornhill is out of the picture so her cover doesn't get blown. She probably told Vandamm's men that "Kaplan" was asking her to contact his handler, and the bad guys gave her the phony address to get rid of him. If she helps get rid of Kaplan, then it deflects attention from her. It surely would be unfortunate for Thornhill, but she probably felt like she didn't have much choice.