The fact that they are the same pearls as we see in "Batman Begins" is just a neat little touch of continuity.
They didn't look like the same pearls. I don't remember large pearls in the center.
My question is: if the night Dent died was the last time Bruce was Batman and he wants to give it up - being on the run and all - why would have built the new Wayne manor with a batcave at all? Not to mention that, if he didnt, the contractors he hired would have gotten suspicious.