First, you need an article - probably the - before "hotel".
Second - both are possible, but I find the continuous "How long have you been staying" more natural - probably because the question is about length of time, so it makes more sense to use the form which focuses on the extended activity (or state).
As to your second question: using the perfect means that there is relevance to the present; so much the most likely interpretation (of either form) is that you are still in the hotel. I can imagine the first ("How long have you stayed in the hotel") in a case when your stay in the hotel is finished, but it is seen as part of something that is still going on - perhaps you are on a trip, and have stayed in other places since the hotel - but I'm having difficulty coming up with a plausible context for it; so I think it is possible, but not likely.