SB's hands were not "cut off". Only the fingers were missing which could be consistent from having them blown off from him covering his face or head when he was shot.They also found a jewelry piece on him. So much with hm knowing he was going to get killed and leaving behind his jewelry. He could have been summoned to a meeting by someone who he knew and then he was wasted.

Here is the report from the Last Godfather:

Body of an unidentified victim of a homicide, discovered 8-12-82 in a remote area within the confines of the 122 PCT. The deceased was found wrapped in a Bellevue Hospital Mortuary Bag.
Adult Male, White, about 5'7", Slim build.
Death by gunshot wound to the head.

When the police pulled the soggy corpe out of the mud and laid it on a bed of leaves, it was unrecognizable. An autopsy conducted the next day found the body was so decomposed and filthy, the skin color was difficult to determine. The entire body is blackish in color, with tan-white greasy areas. The medical examiner had trouble telling if the dead person was a man or a woman. The external genitalia are consistent with those of a male. They are very friable and are falling apart on examination. The body's fingers were also missing
The eyeballs were sunken, the nose decomposed; the tongue was protruding from the mouth. A full body X-ray revealed "metallic fragments" inside the man's skull, which was then cut away for further inspection. A deformed bullet was found in the right frontal area of the brain. Eventually, the medical examiner was forced to resort to dental records to identify the body. Five days before Pistone would take the stand, the medical examiner made his determination: the dead man was Dominick "Sonny Black" Napolitano.

The dirt-covered man's clothing included a dark pair of trousers, a dark V-neck T-shirt, a pair of slip-on leather shoes and a leather belt. ALSO, a metal bracelet with chunky, flat links worn on the right wrist.

(The Last Godfather book)