First of all, the Chemistry upgrade in Age IV is supposed to add 20% bonus damage to gunpower units. But this bonus damage is not applied to Nest of Bees.
Chinese gain access to this upgrade for free. But this upgrade does not improve the Damage of Nest of Bees despite being a gunpowder unit. Other upgrades which increase the range of gunpowder units however do apply to the Nest of Bees. Clearly, this is a bug. As proof: See images below.
But there is another bug: Nest of Bees are supposed to deal 8x8 damage in Age 3, while a Mangonel deals 12x3 damage. But there is no way Nest of Bees deal 64 damage in practice. It looks like half of the shots are simply missing and deal no damage at all. Please investigate this bug.
Its difficult to explain exactly whats going on since I have not quite understood the problem.
Please test it for yourself.
At this point Mangonels are much stronger than Nest of Bees since they deal reliable high damage. Nest of Bees do not deal nearly as much damage as Mangonels from my experience despite being a special unit thats supposed to be stronger.
Images as proof:
This is how it looks in Age 3:
And this is how it looks in Age 4. Damage number is unchanged.