As a general answer, they are equivalent. The two questions ask for an explanation or a justification of a prior statement.

"How can you tell?" is asking for evidence - what features make you believe that answer, what makes you come to that answer/conclusion. "Why do you think so?" is very similar, maybe it is more about the process - what are the reasons or thoughts that make you believe the conclusion/answer? They are very similar questions, asked with different words. It could be simply the style of language used by that person. Another person has a different style/way of asking about situations.

...between the following two sentences* I don't see too much difference although with how can you tell a lot of the times it's followed by "the difference". How can you tell the difference? Hope this helps.