I think you may have misinterpreted the definition of the 50-move rule. The rule applies to any phase of the game, and it's applicable even if many pieces have been captured. In fact, it's more likely to happen later in a game when not many pieces are left on the board.
For example, this recent game between GMs Gata Kamsky and Mickey Adams went 94 moves before a draw was agreed, with only 7 pieces on the board. And if the game had gone on for about 4 more moves, it would have been declared a draw due to the 50-move rule. (The last pawn move was on move 47, and after that, they were basically just moving both knights and kings around on the board ad nauseum.)