1. From my experience capping is just like World of Tanks. If a ship was recently hit, it has little capture points. When you hit it again shortly after, it won't go down a lot. It could also be that there is another ship sitting in the capture circle that hasn't been spotted, like a sneaky destroyer.
2. It seems that the damage that is inflicted by AP shells depends on if it has penetrated or not. 3 things can happen when an AP shell hits a ship. It doesn't fully penetrate, in this case you will do significantly less damage. It penetrates, in this case you will do lots of damage. It overpenetrates, in this case your penetration is so high that the shell penetrates one side and also fully penetrates the other side. You will also do less damage in this case.
3. This is most likely lag. I've not experienced this.