Nightfliers are low in HP, and lacking on the defensive side: one physical attack, even from Mack, will probably be able to take them down. Magic, whether Force or Flara -- maybe even Flare --should also be able to drop them. The thing is, they can actually hit fairly hard (a little more than 200 damage), and they come in large groups. Your best way to handle them is just have all of your party members take out a separate one; that's five in one turn. You should believable be able to kill one, maybe two before they get to attack. So you'll take some damage, but not too much. Overall they're not a big threat. More realistically, they're just a way to cause you to run low on MP while traversing the Black Cave.