A google search shows “unkempt silence” has been used in at least two different novels. I read the sentences in which the phrase occurs. It doesn’t make me any wiser as to it’s meaning. To me it’s nonsense - amusing nonsense.

If you're referring to a silence as a 'xxx silence', this isn't a metaphor. A metaphor is when you refer to one thing in terms of something else, e.g. 'He is my rock'. It could be a personification, as 'unkempt' refers to people. If a person is unkempt, it means that they haven't taken care over their appearance. Literally, it means that they haven't combed their hair, but it can also mean that they look generally untidy and dishevelled - as if they had just got out of bed. That said, I haven't a clue what 'unkempt silence' could possibly mean. It doesn't make a lot of sense, even as rhetorical device. Sometimes people just put words together for the sake of it.

I have never heard of 'unkempt silence". I think it is more likely you are referring to an uncomfortable silence which is simply a descriptive term.