Why would an endocrinologist not prescribe indapamide with my atenolol?

No reason: Only your endocrinologist can answer this question as this is specific to you. Indapamide can be used with atenolol (granted there are better alternatives) so there must be something about you that make him/her worry about putting you on both pill.

Need more info: It's hard to answer the question without knowing what you're treating. If hyperthyroidism is the underlying problem, then beta blocker therapy (i.e., atenolol) is often sufficient, and diuretics (e.g., indapamide) are usually unnecessary. These types of meds are often prescribed together in congestive heart failure, but they don't have to be. Discuss your concerns with your doctor.