it's so the bagel cutter blades do not wear down. A different blade is used, coming from either side of the bagel, compared to bread and other baked goods; when the blades come down to cut the bagel, they go through from either side and they found it was causing too much wear on the blades when pushing them all the way through, since they would of course make contact.
The solution to this was to stop the blades at the midway point, which still allows the consumer to easily finish off the cut themselves, while at the same time conserving the blades for a longer period. Some companies do a better job than others, but generally i do not find it to be too difficult to pry the two halves apart and if it keeps the cost of bagels down, i'm all for it.
Kt