How come shellos are considered the same species despite having different colors and traits depending on habitat, but latios and latias are considered different species? Is it just based on the sounds they make?

Unlike Latias and Latios (or male and female nidoran, for another example), every breed of shellos is genetically similar enough to be considered the same organism. The only reason why the two known varieties look like that is because they adapted to their respective waters to do so, but neither adapted so drastically that they created an entirely new species.

In other words, it really comes down to genetics, anonymous.