I'm not sure why this hasn't really been done in practice but it shouldn't be to difficult to figure out how to do correctly.
In most ATM's the computer hardware and interface connectors are also all housed in the top (mostly plastic or low-quality cast metal) shrouds (as opposed to the currency locked in a safe). Traditionally wafer locks were also used to secure this section however they are slowly migrating to higher security locks like Abloys.
ATM manufacturers may want to take a look at slot machine manufacturers for clues on how to harden machines against tampering.