Yes.
Are the kittens eyes still sealed shut?
Yes.
Someone suggested that a new male might have killed them. After thinking about it, there was no wounds anywhere on any of them. They weren't deformed or anything either.
Well since you said this is her 3rd litter. Then is likely she gave birth to these kittens too fast and that she could not stimulate them fast enough before she gave birth to the next one coming. (too many kittens being born too fast for the mother cat to keep up)
There has to be more kittens and you really should try to locate the rest of them. If you see her out in the open watch where she goes. If she is away from her babies the babies will cry out for her.
One option is to call animal control and have them locate where the rest of the kittens are.
There could be as many as 5 or more kittens that did survive. My guess is the kittens are 5 days old or younger since they still had their cord stubs attached.