I think en-suite bathrooms are brilliant for guests and children - who then don't clog up the main bathroom and get some degree of privacy.
I do agree that DH who (occasionally, ahem) has to get up in the night to nip to the loo, does wake me up. But in fairness he would wake me up whether he went to the main bathroom or our en-suite.
I don't think a house can have too many bathrooms, frankly