Oh, that's a great book. I didn't realize the English in it was so difficult. "Conscientious" means "always careful and thorough, does a job with attention to every detail." "The highly conscientious" means "all the people in the world who are high conscientious." Her job is to inspect the truck. Because she is conscientious she has "random suspicion" that the people in the truck are trying to sneak something in. The narrator says that all highly conscientious people show "random suspicion." They are suspicious even of perfectly innocent people. Innocent people find it "wearing," tiring, annoying, frustrating to have to justify themselves to "the highly conscientious."

Conscientious means to do something very well or thoroughly. Attention to detail. "Which makes the highly conscientious..." means "which makes those who are sensitive and attentive enough to notice (it)..."

the term highly conscientious means that someone pays good attention to detail and does EXACTLY what they should do. The sentence as a whole is saying that this trait is 'wearing' or tiresome.