Unless something has changed recently they don't charge you to fix a laser that can't read dual layer discs, warranty or otherwise. For any other problem you would usually have to pay. NoA historically had great customer service and sometimes they would fix things for free anyway.
I believed they changed, Nintendo wanted to charge my friend $85 to fix the drive. They told him, it's out of warranty, so they need to charge him. However, they fixed his 3DS for free because it was in warranty.