Why didn't the cops investigate Richie Whelan's murder?

Both Marv and Eric are now dead. So the cops don't actually know anything new based on that (aside from the one cop that knew Bob was the guilty one all along). So I'd say there's no new 'clear evidence' to act upon. As to why they didn't investigate earlier, I believe the issue was that the hospitalization alibi wasn't shared information between the policing departments. This seems common both in movies and real life where even though departments are seemingly on the 'same side of the law' there is internal competition and conflict between them preventing open sharing of data.

Detective Torres "knowing" what he (thinks he) knows is not the same thing as having evidence. No body, no witnesses, no direct corroboration = no arrest. Torres simply lets Bob know that he's on to him.

This is the second time I've seen people comment about the ending. Lehane's original short story, Animal Rescue is available online. You may wish to read it to get more insight into Bob's personality, state of mind and motivation. That would resolve this and change POV on what happened after the fade-to-black.

You may also wish to rewind to 3 other times where Tom Hardy's face understatedly tells it all. Notice his eyes when Torres confronts him on the docks after he's just disposed of the arm, notice his face and wording after confronting Marv and the moment of absolute decision after Eric tells him he will kill Rocco. It's all right there in his eyes, face and posture. After looking at those, then re-watch that final scene. The look on his face when Nadia reappears is one of relief. Lehane described Bob as profoundly lonely. I took this to mean that he had self-sentenced out of guilt, but the short story shows that Bob has always been lonely and isolated.