Well they both indicate that the speaker misses you. However, 'still' and 'though' have different meanings. "I still miss you" = I continue to miss you. "I miss you though" = "But I miss you". So they are not interchangeable.

Adding to what Claire said, “I still miss you” can also mean “I miss you even so”. For example, this conversation: 1: “I have been a terrible friend” 2: “Well, you could have been nicer at times.” 1: “I guess you don’t want to see me again, right? 2: “Wrong. Difficult as you may sometimes be, I still miss you. “