So this was actually super fun! I found myself zoning out and just going hard on trying to fill the honeycombs up. I've left a couple longer reviews today so I'll try to keep this one shorter. 1. You are one of 2,200 people who submitted out of 17,000. That alone puts you in the top 10% of devs and you should be proud as hell of that.
2. The game loop is absolutely addictive and very fun.
3. I didn't understand what actually provided the Genes for upgrades or what many of the upgrades would do before being purchased.
4. I could never make it much further past year 1 because the game would hard lag out. Your engine is Godot so I imagine it has something to do with keeping most of the logic in what i imagine is physics_process of the bees. If you are not polling the agents or using a return once they have a task assigned, you are literally making 1 call per frame per entity. At 60FPS that has your little bees making 6,000 calls every second with just ten of them on screen. Thats likely your bottleneck.
If you fix that bottleneck and add a bit more ui polish for the player, I think you've got a very fun incremental game here that I could definitely hyperfixate on as i fall asleep or avoid work during the day lol