The Joy-Con IR camera is an interesting addition that must be for more than champagne shaking. Why do you think was the primary intention? The most obvious to me would be to use its basic depth sensing and pattern recognition in a fashion similar to an optical mouse. This would allow the gyrometer drift to be corrected seamlessly, rather than requiring periodic placement on a flat surface.
Getting more abstract, the camera could be used in conjunction with cards or toys that have certain IR reflective patterns. This would allow a different style of AR than we've seen before. Combining this with HD rumble could lead to trippy effects. For example, placing a fire card on a wood block could lead to smoke billowing out, which could be felt when moving the controller over the set. A tactile puzzle solving game could be developed around this idea.