Why did they choose this as their code phrase?

Firstly, I'm not so sure that this is a "very obvious thing". The Volkswagen Karmann Ghia ceased production in 1974, whereas Cars 2 was released in (and presumably, took place in) 2011. I'd expect that most people nowadays don't even know what a Volkswagen Karmann Ghia is, let alone that it was air-cooled.

Secondly, think about how strange the situation is. A woman you've never met before has just come up to you, out of nowhere, and told you an obscure car fact for no apparent reason. I expect most people would be extremely confused by this, even if they do happen to know why a VW Karmann Ghia has no radiator. To use your example:

That's like I'm an agent and tell another one "Apple falls from the tree"

If I wasn't a secret agent, and you came up to me out of nowhere and said that, I wouldn't say "That's because of gravity". I'd say, "What?"

The only reason Mater isn't confused is because he's... not exactly normal, for want of a better phrase. He therefore offers a sincere explanation, and unknowingly convinces Holly that he's the agent she's looking for.