You are probably right about the pinholes and the cause-n-effect as it relates to using an acid stop bath. To be honest, I never bothered tracking down why I was getting the pinholes because I stopped using that particular film. Overall, I would say that I started using a water stop mostly due to my use of PMK for many years followed, more recently, by Pyrocat HD; and the fact that the dilution I was using was so weak it seemed pointless to continue using the acid.
As with most things photographic I guess it comes down to: whatever works for you.
Thanks, though, for the clarification that the pinholes were probably not caused by the acid stop bath. Should I ever experience this issue, again, I'll look elsewhere.