First id think it was timing chain issue.
Except that the plugs don't move, so timing chain wouldn't result in the plugs being hit. Valves, yes.
I'd say stretched rod, the chance of both plugs being smashed shut by piston debris seems pretty small. I can see the plugs being damaged by being hit from random directions, but smashed shut...that sounds like piston contact to me.
No idea how it could possibly be running fine after something physically damaged the plugs. However, I do know of a Procharged 6.1L that had part of a piston break off (Apparently a known issue with some stock 6.1L pistons when adding power?) and get spit out the exhaust that still seemed to run fine. I was next to him when it happened. Didn't last long, though. He's torn into that engine at least a couple of times that I know of since that happened.
The moral is, don't assume everything is ok. Check it out with a scope or take it to a shop that knows what to look for, if something is busted then it's only a matter of time before more damage is done.