I had "Doom ships" using medium hulls with 220 of doom ray in each and no defensive capabilities. At first I created fleets of 7 Doom ships. When attacking the enemy that had large hulls, 30 shield and 160 of black hole drivers. The single enemy ship was always able to destroy all 7 ships of my fleets even if I had the first strike. Then I tried using a single "Doom ship" fighter to attack it, and guess what? I won the battles every time. I wiped out the entire enemy empire with one single ship!
Ok, first off, when you see the combat what you are actually watching is a animated version of the dice rolls for damage. So, visually, it will be different than what you might think of as "normal". When you watch the combat you are seeing your ships roll for damage first and then the enemy roll for damage. Since the combat is supposed to be simultaneous the enemy does not blow up until his shots are displayed.
So, lets look at the fight. You had 7 medium hull ships each capable of 220 points of damage against one large hull ship capable of 160 points of damage. Any one of your ships is capable of putting out more damage than the enemy has hit points. So, only one of your ships fires because once you do enough damage to destroy the enemy ship there is no reason to make the other damage rolls. Your opponent has enough weapons on his ship to make a damage roll for each of your ships and since each weapon he has is strong enough to kill a ship outright that is exactly what happens.
Think of it in terms of a tank (opponent) vs. infantry (you). Say each of your guys has an anti-tank missle. They all jump out and aim at the tank but only one guy fires. The others do not since they know the one missle will do it in. Meanwhile the tank, with it's machine gun, gets to shoot at all the exposed infantry. The machine gun is more than capable of killing all your guys and it does. So, solution is, send one anti-tank missle guy against one tank.
As for "being cheese", that can mean a lot of things. In this case it would refer to tactics used by a player or AI that, while following the mechanics of the game, violate the spirit. For instance, when a ship on ship battle occurs if both attacker and oppoent do enough damage to kill each other the attacker gets to survive with one hit point left. There is currently a glitch where instead of surviving with one HP the attacking ship is restored to full HP. A "cheesy" tactic would be to take a almost dead ship and attack a full HP opponent knowing your ship would come out of the fight with full HP.
Hope this helps.