I had been taking Omeprozole for about 5 years before my SFN started. Whether or not it has anything to do with getting SFN I'm sure I'll never know. Like most people, I have a number of things that could have caused it or at least been a contributing factor.
When I realized that the omeprazole could be a contributing factor, I considered quitting it. However, I do have significant gastric reflux. In addition to the obvious pain of heartburn, there is the risk for erosion of the esophagus - eventually leading to esophageal cancer. (There is a history of this in my family.) After weighing the risks and benefits, I decided to continue taking it. But I am supplementing all the things Mrs. D mentioned that can be affected by the lack of stomach acid.
As with pretty much everything related to PN, there is no clear cut answer. You'll have to look at your own list of risks/benefits and make the best educated decision you can. Good luck