Strange indeed!! First of all, my kneejerk reaction would be, that they might of been familiar with what was underneath the tarp. I don't know how secluded your father in laws place was, but attempting to steal something that big, without knowing what it was to begin with well, may have been a long shot.
Secondly, and if the robbers knew what was underneath the tarp then, they might of personally known your father in law, or some part of his family. (directly or indirectly) This may explain for number one, why they returned the boat intact, (minus a few parts) AND why they felt confident in returning it without getting caught. Kinda like a combination of respect for your father in law and his family, plus a general confidence of the "lay of the land."
I know gold is well over a thousand bucks an ounce. Was there anything on the rudder or next to it, that was possibly of any value? Something that could easily be stripped or taken apart quickly, for a substantial profit?
A Catholic church down the road from my house was robbed a couple weeks ago. It's funny how they never catch the person who does it either. It doesn't matter which Catholic church it is either. It's ALWAYS the gold plates, cups and challices they use during their mass, that gets ripped off too!!
...did I say, that the price of gold is well over a thousand bucks already?
Anyway, it sounds like somewhat of a happy ending to the boat anyway. (seeing as it could of been far worse)