When the bees land they make flowers. The bug-spray can't move to where there are flowers. So, the more bees that land the less space you have to shoot. You can get rid of the bees and the honeycombs with the bug-spray.
Leaving the honeycombs is useful because after the hummingbird collects from them, this gives you more bug-spray. However, leaving the honeycombs makes the bees land faster. If the bees cover the bottom of the screen with flowers or if you run out of bug-spray then you lose.