I hope an American can give you an authoratative answer. But I guess that the phrase was used before Hawaii became the 50th state in 1959, because as you say Alaska was "above" (ie north of) the other 48 states; and that the expression has continued to be used, though it is now not geographically accurate. Also, other phrases, such as the "first 48" or the "mainland 48" might not be considered politically correct, as they might imply the precedence of the earlier 48 states over the later two,