Andrew,
I have heard this from other patients of mine. I do not believe it is the Water Pik that they are worried about but what some patients place in the resovior. The use of a water pik reported in several studies from the '90's was stated to provide no significant difference in removing debris from the teeth and/or oral appliances than a vigorous rinse with water.
The studies suggested that the water pik itself may have increased the patient's own motivation to focus more energy on proper oral hygiene.
So, if the use of the water pik with only water or an alcohol free mouth rinse is used in the resovior then In my opinion I would suggest that you are not causing any adverse affects.
Cheers,
Mike