Hi. Great questions. "BEES" is just the number of bees available vs. the number of bees in a hive. Player starts with 5,000 available bees. If all your bees are in a hive, then you can't use them for combat or other actions.
HD (Hit Dice) and ML (Morale) are both taken from the DURF rules. They relate to combat.
From Durf:
NPCs have an ML (Morale) score and make a Morale Roll when something manages to shock them (they meet more resistance than expected, their leader is killed etc.). To make a morale roll, roll 2d6. If the result is higher than the Morale of the NPCs, they will flee or attempt to parley.
Player characters start with one Hit Die (HD) - a d6. These are rolled when the character is wounded to determine if the wounds are fatal. [When] a creature takes damage, the damage first reduces their Armor points. If no Armor points remain they take the remaining damage as Wounds. Each time a creature receives Wounds they roll their Hit Dice (HD). If the result is less than or equal to the Wounds they have accumulated the creature dies.
Now that the game jam is over, I'm working on a more comprehensive set of rules that will clarify and hopefully streamline some of this. I hope to share that soon! Until then, it's probably best to refer to Durf for combat and more detailed gameplay questions — or use your favorite system. The Beekeeping mechanics should work with most game settings.
Thanks for your interest and kind words!