Hi,
PPI like prilosec are relatively safe medications.
It is only about 2 decades since the first PPI omeprazole was introduced. So not many studies are there which discuss about the long term effects of these medications.
The possible long term effects are -
1. Formation of gastric polyps
2. Osteoporosis due to interference with absorption of calcium
Just take care for long term use of PPIs. They are reportedly facing complains like osteoporosis in patients over 50yrs age and possiblities of hip fractures. PPIs are not recommended on a permanent basis. However some physicians do.
If you have GERD there are dangers of not controlling it as well. I recently learned it is possible to get pneumonia from acid reflux even with people who don't realize they have it. I think the majority of them are safe and I wouldn't go a day without mine. Just eat healthy and take multi-vitamins.