Yes. The mentioned deficiencies are true.
If the condition for which it is being used is Gastroesophageal reflux disease (GERD) then surgical correction in the form of fundoplication will be a definitive treatment.
The effect of all drugs used is to reduce acidity in stomach.
However, acidic environment is an important factor needed for absorption of
calcium,magnesium, and other vitamins.
Hence no drug can prevent these side effects.
Either you take supplements or consider definitive surgery