No they do not. When creating an iPerceptions Certified Survey, you can choose to add every questions that is provided within the Survey Creation Wizard, and you will still have your entire limit of custom questions at your disposal.
Custom questions are considered the ones that you add through the "Add Question" menu.
Click here to learn more about adding a new question
Click here to learn more about the Survey Creation Wizard
Click here to learn more about the number of custom questions you can create based on your iPerceptions plan