I feel ashamed - my english is still so poor that I am unable to explain this one properly...
Let me try once more.

The poin is, that you don't count the edges. (Hence, it does not matter that you are missing some when rapidly oscillating while the encoder is not moving).
You take samples at a steady pace,independently from the signals.
The electrical + mechanical design of the encoder (assuming its electrical connection into the system does not introduce extra noise) must be such, that there is some minimum time between the transitions, where both signals are steady and clean (at a given maximum rotation/movement speed) (and of course, only one of the signals may change at a time).
Then if you sample at such a rate that there is guaranteed at least one sample in that "clean area", you won't miss a single count.

Of course, some noise filtering can be done by any means, but it is unrelated to the principle above.

Jan Waclawek