A lot of gyms don't even have puzzles: Pewter, Cerulean, Rustboro, Fuchsia, etc. So yeah, gyms don't always need puzzles to be good.
And by the way, you CAN make some cool ones in Super Secret Bases like teleportation tiles, invisible dolls, floor holes, turning the light off, etc. The more flags you collect, the better puzzle tricks. That's a lot more in comparison to what some real gyms offer, like the mentioned above.