I had read about this place on HappyCow, and was here in November 2012 for lunch. Here's my Naked Cafe review.
Naked Cafe is located in Carlsbad Village which is quaint and near the ocean. The plaza it's in houses many other shops. There is both indoor and outside seating. On the day I went, 2 musicians from the music shop (also in the plaza) played string instruments in the courtyard for all to hear.
If you do not care about cross-contamination or don't think about what goes on in the kitchen, then you would be okay eating at Naked Cafe. As with most non-veg restaurants that provide veg options, the food (meat + veg) is prepared in the same kitchen, on the same grill, using likely the same utensils.
The menu is Southern California American fare: egg and toast kind of breakfast, wraps, sandwiches, burritos, and the like. Dairy, eggs, and meat are prevalent; however, you will also find vegan options. Grilled tofu is an option as accompaniment to a stir fry, a rice bowl, wrap, and build your own sandwich. Soymilk is on stock.
I ordered the "transcendence wrap" which is chili grilled tofu in a tortilla wrap served with a side of quinoa and salad greens. It was very tasty. The coffee is organic and tasted okay.
If you are vegan, let your waitstaff know.
For a town like Carlsbad, which is predominately upper class income and caucasian with no pure veg restaurants, Naked Cafe is about as good as it gets, and it's all right. The owners also operate a few other Naked Cafes in the area (Solana Beach, Encinitas, San Diego).