My Muscovy's were all hatched here and they do all fly, but usually its for a reason. Over a tall fence if the hens are being fed and they want some, about 100 metres over some gates to the larger pond, or when there is a duck on eggs and the drake is looking for her he will fly quite far and quite high to try and spot her. Or of course if they are being chased (by an escapee terrier usually)..
I didn't realise how well they flew when I first got them and I lost a few, so think clipping their wings is an excellent idea. For older birds that have been living with you for some time I wouldn't bother top clip after they moult as they will know there home. Younger birds hatched there won't want to wander too far either.
I wonder if you clip meat birds wings will it affect the size of the breast muscle though?