Does using flaked salt make a difference when using it in cooking?
Salt (Sodium chloride) is salt. As a topping, flakes are commonly used purely for presentation purposes only. The taste is the same, but gets more intense as the salt particles get finer, so use less if the salt is in powder form

As an ingredient, use any form you are happy with, and is economical to use. Once salt is dissolved into water it will be identical to any other form of salt

For health reasons, finely powdered salt is preferable as much less is required to impart a salty taste