I work at my college in the computer labs. Currently half of our campus computers have flatscreen monitors. From my experience, the flatscreens are nicer, but people touch them and press on them, and they don't last as long. Women have these deathly fingernails that they will press onto the screen causing distortion... trying to express why they can't get some .net crappy app to compile. I think it would be unwise to get rid of a CRT educational model... they are alot more durable. That said, I think apple also needs to expand their desktop offerings. Currently, you've got the overpriced all-in-ones and the expensive (although not nessesarilly overpriced) powermacs. IMO there is a big hole right in the middle. You guessed it... the cube.
Anyway, i expect the eMac to evolve... not dissapear. Just because of its affordability (extremely rare in the apple world of computing) and its durability.