C'thun and Yogg can very likely return in some form. Know Your Lore over at WoW Insider uses the Y'shaarj story to mean that the Titans imprisoned the rest because they knew Old God death could cause even worse problems. It stands to follow then that we no more killed C'thun and Yogg'saron than we did Ragnaros in the Molten Core.
Here's what you're actually told by the Klaxxi:
Kil'ruk the Wind-Reaver says: When the usurpers came - the ones you call "Titans" - Y'shaarj was destroyed.
Kil'ruk the Wind-Reaver says: His last terrible breath has haunted this land ever since, but the shadows he left behind are mere whispers of his former glory.
Kil'ruk the Wind-Reaver says: I tell you now, because you have earned this warning.
Kil'ruk the Wind-Reaver says: Your gods are not your gods, outsider.
Kil'ruk the Wind-Reaver says: If the Old Ones ever return, we mantid will once again stand by their side.
Kil'ruk the Wind-Reaver says: The wisest among you will do the same.
What he's saying is that the Klaxxi are on the side of the Old Ones despite the death of Y'shaarj.
Regarding the eggs in the chamber, those are likely princesses.