I believe beam weapons reduce shields by how much damage they do. Point defense destroys a missile for each point of point defense you have. A ship with 20 shields is hit by a beam weapon that does 4 dmg, the ship now has 16 shields. A ship with 20 pd with 10 missiles coming at it is reduced to 10 pd.
I do not use armor since pd is so poor so I dunno about that.