The bees have a similar effect to rotten cows thrown from trebuchets I think - they hit the morale of the units affected quite a bit. I'm not sure if they also cause casualties or give attack/defence/stamina penalties to the affected units.

I don't think they do much damage, but imagine if a load of bees were thrown at you, getting under your armor, etc. You would panic and go crazy. So I guess it damages moral more than anything.