“If you have any questions” is correct, because the word “question” is a countable noun.

When a noun is countable, we always use the plural form after “some” and “any”:

• I bought some flowers.
• We don’t have any questions.

We only use the singular form after “some” and “any” when a noun is uncountable:

• I bought some sugar.
• We don’t have any advice.