I'm Greek and I'll be the first to admit that the police can be bandits (putting it mildly) at times as the OP mentioned.
While plain spotting is a well documented hobby, there is no excuse for taking pictures of airplanes in areas where there are more "no photography" signs than "no smoking" signs. On top of that, noting the plain numbers in crossword puzzles is not exactly "openly" collecting data.
As for spies, i don't thing they all drive Aston Martins, wear black suits and sunglasses.
I'm not trying to defend the actions of the police. They should have let them go with a warning, perhaps confiscate any cameras or film rolls if they wanted to cover their backs, but lets call a spade a spade. These guys hadn't done their homework. They went on holiday to a place where photographing military installations (most airports in Greece are classed as that) is prohibited, they found out they shouldn't take the pictures but they went ahead anyway thinking they can get away with it.