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Using ReplaceAll as follows:

a = {{{0, 0}, {1, 7}, {2, 0}, {3, 2}, {4, 7}},
     {{0, 0}, {1, 0}, {2, 1}, {3, 2}, {4, 7}}};

a /. x : {_, 0} /; x[[1]] != 0 :> {x[[1]], Na}

(*{{{0, 0}, {1, 7}, {2, Na}, {3, 2}, {4, 7}}, 
 {{0, 0}, {1, Na}, {2, 1}, {3, 2}, {4, 7}}}*)