It's likely alot cheaper to make accessories with an ir port than bluetooth (for example the pokewalker) so i would assume it's likely to be used for small little things such as that (and hopefully GBC), whether or not it really gets used much is another matter.
As for if the 3DS has bluetooth, the operations manual does not have bluetooth listed in the index, and i cannot see any bluetooth logos on the box or console. So it's seems safe to say it doesn't have it.