Whoa!
I've
never heard of dogs wanting to be fed 2-3 times in the middle of the night. No offense, lol.
I would put a stop to that immediately. That's just nuts.
How much exercise do they get during the day? Exercise makes them hungry... so take them for a nice, brisk walk in the morning (if possible! if not, at least a 30min-1 hour walk a day at some point) and when you get back, feed them their kibble mixed in with some of the wet food. That could start your morning schedule. Make them work for their food! Make them sit before placing the bowl down. Don't just cater to them when they're whining in the middle of the night. Plus, doesn't that make for an awkward potty schedule?
All I know is I would never in a million years be waking up in the middle of the night for my dogs to be fed. You've already created a bad habit so it's going to be more difficult to break. Ignore them in the middle of the night! If that doesn't work ... take action. I would use coins in a can and shake it whenever they whine or bark for food. Or use a spray bottle and do a quick squirt at them to get them to stop the whining. I usually would suggest simply ignoring but at this point, it sounds like that may not work great.
I personally give Jackson his breakfast every morning by filling up his bowl with kibble. Usually, every other morning, he gets wet food mixed in as a "treat." Then, I fill up the bowl w/ kibble and just leave it out for the rest of the day. He goes over and snacks every now and then. The kibble is usually gone by 7pm and it stays empty until morning time again. So he's sort of free fed and he never over eats. If, for some reason, they are scarfing down their food... just don't put as much in the bowl. I put the recommend feeding per the back of the bag of dog food and put that in Jackson's bowl so I know he's not eating more than he should.