It can be used in both meanings, subtle meaning indirect, undertoned, but also delicate, gentle, yet recognizable.
Compare:
It was a warm, calm day, with a very subtle breeze. (= calm wind)
It took a while for me to fully understand her, she was very subtle about it. (= I finally understood her point, but it wasn't presented directly)
As regards negative/positive I think that is to be taken from the context, the word subtle itself having neither positive nor negative connotations, simply describing the method, rather than means.