I'm sorry this is happening. I mean no disrespect, so please don't take it that way. However, third graders are usually between the ages of 8 and 9. That is plenty old enough to either learn or already know about life and death. Why doesn't the teacher simply write a letter in regard to the recent "demise" of the eggs and send it home with children, explaining to the parents what happened (so they understand why their children may be sad or need some gentle conversations, etc).
I do remember being that age, and if someone lied to me and replaced a dead chick/egg with live chicks to ease my emotional suffering - I'd be pretty offended (and trust me, kids that age are a lot smarter than what they are given credit for. Many of them will see right through it and be confused - as they are taught not to lie).
I say don't molly-coddle...just tell the truth of what happened. It's okay to let kids be aware of the fact that life is not always rainbows and gumdrops. They'll be more well-adjusted kids because of it.
I would also candle the eggs to make absolutely certain that they're not just late bloomers before I started pitching them.