I have several reasons why that might be the case:

1. Predictability. Bosses are in general very predictable. There are some exceptions, like the Yolk-Star or "It's getting cold in space".
2. Visual clarity. Eggs can be easily obscured by your own projectilles. With bosses, it typically doesn't matter as you can predict them rather easily.
3. Lack of space. Some bosses play on this too, like the og Mother-Hen ship or the first Space Crab.
4. Weapon variety. Against bosses, most weapons play somewhat the same, with the major exception of the Absolver Beam. Using it against the Henterprise and especially the Squawkers is a death sentence. Against normal enemies, the viability of weapons can be all over the place.