Do more relevant ads have a higher CPC? Yes, they have.
The reason for that is simple: They are of higher quality for the advertiser.
People clicking relevant ads tend to buy something more often.
Let's assume you have a website about sport cars, about Audi R8 rims. Your ads are showing funny video ads. Who would be clicking on the ads? Nobody. People clicking on them usually do that accidentally. They won't check out the advertisers products and buy something, they'll just bounce away. Generalizing that whenever your ads are not relevant your clicks are low quality and thus do not pay.
Use AdSense section targeting.