Eric has relatively recently revamped the way the flow commands (cond, start, else,stop) work to get in line conditons working. So I think yes, stores in cond blocks will execute.
You're definitely right that that *.nrg .shootval store line is interesting. It would seem to scale its shot strength based on the amount of nrg it has. I wonder what it mutated from. Animal Minimalis doesn't have any shootvals.