Well there's always a risk anywhere you go. They have high security in shopping malls and hotels not because it's fun to search everyone entering. In fact,the reason I stay at not so nice hotels in Manila is to avoid the BS security of Makati hotels.
As for Dumaguette, until you like muck and critters, I'd pass. Ducomi, the famous pier that was probably the best muck diving in the Philippines is now closed to divers. The corals around Apo Island is pretty and healthy but quite fishless compared to say Bohol.
As for ops, Atlantis has issues with their day trips to Apo. They don't have dinghies for recovery and dive the sites in current and expect you to return to the boat. I had no problems but people I was with went OOA and surfaced about 400m away from the moored boat and showed distress signals. They were ignored and only after 20 minutes of waving did the diver master swim out to get them. yes they kept the boat moored the whole time. I gave them a piece of my mind because of that incident. They had some great local guides but the management is insistent on hiring foreigners for the guests. Most are ok but not good at spotting critters. They have since fired the one we had who messed up dive briefings and was insistent we swim along a reef to make it to the boat vs having the boat pick up. That's the way it operates and most of the other big ops Dumaguette do so too.
As for food, eat at the Eldorado restaurant, it serves significantly better food than the Atlantis Resort. Having stayed at the new Sea Explorers Resort, I'd say you should also consider that resort seriously.