I know that PPIs are implicated in polyp formation, but I have not read anything that suggests they're involved in cyst development yet.
I have taken a prilosec equivalent here in Australia for quite a few years. It and other meds such as Losec (Australian name for Prilosec) and Pariet are proton pump inhibitors (PPIs). Interestingly I also have liver cysts - called simple cysts. There may be no connection of course. But I have read somewhere that ovarian cysts can be connected to PPIs. I also have gastro polyps as a result of long term use of PPIs. To avoid the polyps you might want to consider getting off PPIs once you have the acid reflux under control - and then seriously change your diet to make sure you don't get reflux again (less animal fats, sugars, acid food etc.).