There are benefits to wearing clothing while gathering. For one, you get stat boosts, which will make gathering easier, which will help you level faster.

Also, as you gain XP while wearing gear, the gear's SpiritBond (SB) level goes up. When the SB level hits 100%, you can convert the gear into Materia. (The gear is destroyed in the process.) That Materia can then be attached to other gear to give it stat bonuses. Here's a primer on Materia.

So while you can probably get away at lower levels with gathering naked, there are definite reasons -- maybe even better reasons than avoiding the sight of naked lalafells -- to wear clothes.