The fact that he insisted on a 6 deck shoe seems to suggest that he was, in fact, counting cards. I was under the impression that standard casino blackjack shoes were 8 decks (machine shuffled).
He may not have played as a standard card counter would (as that would make him more detectable), but he still could have made riskier plays when the shoe was "hot" to give him a slight edge over 49.75-50.25
And whether a game is machine-shuffled or hand-shuffled will usually depend on the min bet. The higher the minimum, the more likely the table is to be hand-shuffled, and the lower tier the casino, the lower that minimum is likely to be. For example: the Wynn Las Vegas' $100 min table is machine-shuffled, while Harrah's Lake Tahoe $100 min table is hand-shuffled.
My understanding is that the 6-deck shoe confers a mathematical advantage, not simply a card-counting advantage, over an 8-deck shoe. If you use the calculator here you will see that it improves odds even under basic strategy play:
http://wizardofodds.com/games/blackjack/calculator/
He may not have played as a standard card counter would (as that would make him more detectable), but he still could have made riskier plays when the shoe was "hot" to give him a slight edge over 49.75-50.25