I think the problem with bees is that they're a pain to breed without external mods and anything they make can be created in easier and more efficient fashions. Prismarine, Actually Additions Atomic Reconstructor. Redstone, Red Orchids. Glowstone, Void Ore Miner or Resource(Don't remember if Glowstone is technically an ore). Ender Pearls, Woot Mob Farm. Etc Etc etc.Maybe, maybe not. Having a renewable source of odd things (prismarine for building blocks, redstone, glowstone, etc) can be as useful in late game, if not more than early. Again, if you have other methods to obtain them, it might not have the same appeal.
For oh so long, the answer to, "How do I get <insert item here>?" has been, "Bees."