Different circumstances = different outcome. Maddox was brought on board in extremely poor shape, his injuries were known to be severe and life-threatening. He was alone with a trained doctor when he died. If that trained doctor says, "I did my best, but the injuries were just too severe," why would anyone doubt her word? This situation isn't about an equipment failure that would require an investigation, because Agnes didn't say the equipment failed, she said that Maddox's injuries got the better of him despite her treatment. The EMH has not been needed since, so has not activated to tell what he knows, and there is no reason for anyone to summon him just to verify Agnes's version of events, because they have no reason that they know of (yet) not to trust her.