No, within the context of this game, we felt Storm damage wasn't worth modeling. Even when the historic Mulberry was damaged by the storms, it still proved to be extremely effective and was used until it was sunk. With weather already playing a critical roll, we did not feel it was something to "chance" having the Mulberries potentially eliminated within the time frame of the game (early playtest versions did have a Mulberry damaged/eliminated rule).
Color inside is mainly aesthetic, though it helps to identify the different divisions. I believe all the 352nd units should be the same internal color and I know there is a 352nd errata counter (but don't remember if that is the reason why...).
Do storms damage mulberrys (other than to prevent the landing of supplies on the turn the storms occur?
What is the purpose of the color inside the unit type square. For example, the 352nd Division has infantry units with different colors where the infantry x is.