Certainly don't know why a number of Penzeys have closed but have some thoughts. Retail is expensive - store lease, employees and cost of doing business at a store. You have to sell a LOT of spices to make a store profitable. Maybe some stores simply are not profitable when costs are compared to profits. I also recall they used to publish a magazine but that didn't last long - probably not profitable.
Bill Penzey is no spring chicken. Maybe he no longer wants the headache of operating a bunch of retail stores and wants to emphasize mail order only.
When I did an online search of articles mentioning the close of a location, they all said, calls (to Penzeys) for comment were not returned.