It was just convention, there isn't usually a distinction about the octave, so the 2nd/9 is usually called the "9" same with all the others, 11=4, 13=6. If all the notes are put into a chord like:
C E G B D F A
R 3 5 7 9 11 13
Then the d note is the 9ths of the chord, so no matter what octave it is in, it gets referred to by that. But you are totally right, same as the 2.
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