Thanks, Eigen, for going great lengths to reply my question.I gather you are translating a poem about visiting an absent hermit.
Short answer: As it's a poem, there isn't necessarily a clear and concise meaning to convey. As such, either in or among (or amongst) would work from a grammatical point of view.
Long winded waffling answer: Another translation of the poem I found on the internet explicitly states that the master has gone up a mountain and is thus hidden by thick cloud. While this could be the case in your translation, you should be aware that, as with much poetry, different people may read it differently. What sounds a little odd to me is the mention of being in/among clouds without any mention of altitude. When I read it my thoughts are as follows:
If they were low down clouds, I would call them fog, so…
Are they metaphorical clouds or is he high up?
I'm not saying that you need to make it clearer. I'm just trying to explain why it is difficult in cases like these to provide a hard and fast answer as to which word is correct or more idiomatic.