Thanks everyone. There is some good info here

I rarely see mortar at these open spaces in my area. What I usually see is a thick coating of a tar looking mastic sealing the open spaces to keep the weather off the battens and out of the open spaces. In this case however, all that was protecting the open spaces was the poly-flash looking material which as you can see in the photo does not actually seal anything from (as mentioned earlier) wind driven rain etc.