Nathank, I have not yet come across any restrictions to mountainbikers here yet, but it may just be because of this God-forsaken boring landscape around Berlin. In the woods, I get off the beaten track and use singletrack as much as I can, but the hills here resemble two fried eggs on an ironing board.
I would give my right knacker to be down in the elevation of Munich, as would the rest of the team, as that's where the best and most popular marathons are. At least you have the Alps, Bavaria, Austria, Italy etc. We have Poland and er.. Poland.
In all of the places that I have ridden and raced in Germany, mountainbikers are welcomed and nothing has been said about damage to the countryside (if any), though this might be due to the race routes staying on marked paths. You can pretty much go where you want to. What bike have you got anyway?