The math of shuffling cards almost brought down an online poker empire

One thing that I wonder about is that even with Fisher-Yates, a PRNG relies on a seed value. Assuming that this seed is going to be a 64-bit value, that seed value can only go up to a maximum of 2^64-1 = 18,446,744,073,709,551,615.000, which is still less than 52!.

I know that modern operating systems use an entropy pool. Does this mean that the PRNG is re-seeded for every random number generated, thus making this a non-issue? Or does it just take from this entropy pool once?

No cryptographically secure PRNG has a 64-bit state. If you are not using a CSRNG in an adversarial environment, you have bigger problems.