Does omeprazole effect the absorption of calcium, or vitamin d? or cause any other sideeffects to bone health?

Yes...: Omeprazole belongs to a class of drugs called proton pump inhibitors (ppis) which are a popular treatment of gerd and dyspepsia. When used long term (10+ years) studies have uncovered an association with increased risk of hip fracture believed to be secondary to bone disease (osteoporosis). One must always weigh the risks and benefits carefully to avoid a therapeutic mis-adventure.

Ca++ malabsorption: Calcium malabsorption may occur in diseases that affect the small bowel lining (e.g. Celiac disease), with bile acid deficiency (due to fatty acid malabsorption), with renal disease, hypoparathyroidism, inborn defects in vitamin d formation or the vitamin d intestinal receptor, with gastric resections, and with chronic acid blocker drug use.