Typically, no. But they do random checks at various points, including as you exit the aircraft. The requirement for any visa, however, will be enforced by the airline who will not board a passenger who requires a Direct Airside Transit Visa (DATV) without one, even though they might not come across immigration officers. Otherwise the airline will face a fine.

As the previous poster mentioned, check with the Embassy, particularly as if you're wife is exempt, you may want to remind check-in staff who might be unaware of the particular rules. She should be fine if there is no general requirement on Indonesians to have a DATV, but if it is because of the US greencard, she may need to draw the check-in persons attention to that.