That's true, they didn't have enough evidence to prove intent. Although having a low level staffer who had no business providing government IT services destroy the phones was unheard of, violated the law on how government records should have been handled, and highly suspicious there are also possible "valid" reasons for it, like protecting the information in those devices from being able to be recovered by anyone who dug the devices out of the trash, and the destruction of emails after 60 days could have just been to save space rather than specifically to hide evidence.
They also decided not to go after charges for the nobody staffer who did the deed, and controversially Hillary didn't face any consequences with the FBI saying: "To be clear, this is not to suggest that in similar circumstances, a person who engaged in this activity would face no consequences. To the contrary, those individuals are often subject to security or administrative sanctions. But that is not what we are deciding now."
They also decided not to go after charges for the nobody staffer who did the deed, and controversially Hillary didn't face any consequences with the FBI saying: "To be clear, this is not to suggest that in similar circumstances, a person who engaged in this activity would face no consequences. To the contrary, those individuals are often subject to security or administrative sanctions. But that is not what we are deciding now."