That initial bee hive you were confused about does generate bees in 1.00g, but only in hard mode. There are a lot of differences among the various difficulty levels when you compare the OEM versions to the final.

Regarding the fireball, I tend to assume that it and the blade gun got the axe because they're just not very interesting. They're both essentially more powerful versions of the blaster, and there just aren't any enemies in JJ2 that such a distinction is really useful for. Pepper spray and electro blaster are much more diverse.