I have been taking omerprazole 40mg daily for 6 yrs can this cause health issues?

Few linger... ...past the time you stop the medication--e.g. headache, diarrhea. However, be aware that chronic use can increase risk of osteopenia which does not reverse when Prilosec/omeprazole is discontinued. There may be some effects on magnesium metabolism and risk of certain infections too with chronic use of the drug.