I assume such a large confirmations requirement has to deal with the possibility of chain reorganizations. Unlike a double spend for a regular transaction, where 6 confirmations in one chain will usually guarantee the transaction will be found in all competing chains, for the coinbase transaction (new bitcoins mined) a chain fork and reorg will guarantee that the coins mined on the alternate chain will be worthless.

So it makes sense to expect a large number of confirmations before paying the mining shares. On the other hand, if the pool pays using the mined coins themselves, it should have no risk. So the real reasoning could be a bit more complex.