Will one get in trouble for taking a jailbroken device through airport security?
From me, a US citizen, I wouldn't worry about it at all.

They shouldn't even touch his iPhone/iPod, let alone turn it on. Also, I can't imagine how he could get in trouble over something that is legal in the US (jailbreaking). 

From my experience flying, electronics are just sent through an xray machine. Any search of electronics would make people upset on grounds of the 4th amendment.