People and banks prefer the new notes. Some will not accept the old notes at all.
Edit: To back up my answer: I have been collecting traveler updates from Mongolia and the larger region since 2010. I haven't heard of anyone having their old 100$ notes rejected, but I would not rule it out simply because I haven't heard/experienced it, and I think some kind of rule/habit could come soon to the country. So I advise, anywhere along the Silk Road, always try to travel with new, crisp, unfolded dollars. In Turkmenistan for instance, old 100$ notes are already no longer accepted, and many people across the region are fussy about the condition of the dollars they accept.
