It's true the shield takes all the damage from the first shot no matter how powerful the damage was. I noticed it before and I think my solution is too simple to add into the mods. I use 2 kinds of edited weapons on my ship, and I set first has the speed of say, 2k/s and next use 1.5k/s. They both do good deal of damage, and I was able to take out most of the ship with one shot, since the rounds travels in different speeds.