Generally, no. GameStop typically does not apply adhesive security tags (those white RFID/sticker tags) to 3DS game boxes. The tags are reserved for the cartridges themselves, which are higher-theft, higher-resale-value items. Here's the reasoning.
Individual GameStop locations have some discretion. A store with high shrink (theft) rates might tag more aggressively. If you're buying a specific item and concerned about adhesive residue on the box art, ask an employee—they can usually check or peel it off at purchase.