We have a 6am departure on a Friday morning from Malaga to Munich, should we try to stay at airport or are busses running for 4am ish ride? (How long before flight should we check in? I'm at 2hr ahead girl, is this excessive?) also how long bus or train ride to airport from centrum...if running all night?
Neither train nor bus run to the airport at that time of the morning. There is nothing to entertain in the vicinity of the airport if you stay there, if it matters. Taxi from Malaga city to the airport might be €25 - €30 at that time.
Are you flying Ryan Air to "Munich West"? Understand that "Munich West" is actually Allgäu Airport, in Memmingenberg, on the border between Bavaria and Baden-Württemberg, about 70 miles from Munich. There are no trains directly to the airport. There is a 12 min shuttle roughly every hour to the train station in Memmingen. Bus and train together take about 2 - 2½ hrs to Munich. There is also a commercial shuttle all the way to Munich. These take about 1½ hr and leave every 1½ hr.
This is not going to be very helpful. We flew out of Malaga a couple of years ago. As I remember the airport there is very little development around the airport other commercial buildings, warehouses, etc. It is a nice airport. At that time of morning, and a domestic flight, I would think an hour and a half would be more than adequate. Your hotel probably would be your best source of info for getting to the airport. Have them arrange the taxi.