It came out in the trial that Nick removed a gun off of Michael after Michael was strangled and he gave the gun to DiFronzo.
I believe that Nick was at the murder scene. Fosco said that the feds at one point did search the basement of the house in Bensonville but didn't find anything incriminating. The feds took Nick around Bensonville to see if he could point out the house but Nick couldn't remember. Nick didn't drive to the house on the day of the murders and it happened over 20 years ago so it's believable that he couldn't remember the exact location.
Aiuppa and Cerone didn't tolerate any high profiling in the Outfit. They ordered a lot of brutal murders.