The idea that Nomad could repair a dead human with a beam of light is just silly.
But how do you define "dead?" Even today, it's possible to revive a clinically dead patient without permanent brain damage if they're treated promptly, within a matter of 3-5 minutes at normal body temperature, up to twice that if the body temperature is reduced by several degrees. Both McCoy in "Shore Leave" and Scott in "The Changeling" were clinically dead for only minutes before their revival, so it's not that implausible even by today's standards. The main obstacle to recovery from clinical death is the rapid accumulation of ischemic injury in the brain; otherwise, most parts of the body can survive hours without blood circulation. If advanced medical science had a way to minimize or reverse that damage to the brain, it could certainly be possible to revive people who had been clinically dead for a longer period of time.
As for using a beam of light to perform a medical procedure, we do that today with lasers, and there is research underway into other potential techniques employing light to activate or regulate chemical processes inside neurons or other cells. Or it could be that the "light beams" used by Trekverse medical devices (like those seen in the 24th-century shows) are some kind of array of micro-tractor beams doing fine manipulation of cells.
My definition of dead is when McCoy says "He's dead Jim". At that point I'm convinced that the person is actually dead and that McCoy isn't simply being lazy.
Of course, that doesn't work when it was McCoy that was the dead one.
I see your point about Nomad but Nomad has always bothered me. He could do too much from firing energy equivalent of 90 photon torpedos to reading (and emptying) minds as well as raising the dead. But, if we put that down to advanced alien technology then it works. However, it's still part of the idea that death in the Trek universe isn't permanent.
Would it be possible to being back Duffy after Wildfire? Sure, just bring in Q. However, it would cheapen his sacrifice and risk turning Trek into a soap opera.
Could you find a way to restore all the people killed in Destiny? Same answer.
Once that particular genie is out of the bottle it's very hard to get it to go back in. The fact that Janeway was last seen in the company of a Q just reinforces the point. Why should we care when a character dies?