So I just encountered the Legio for the first time since updating, and I've got Hel-Hammerheads one-shotting paragons at zero flux with their shields up. And it's not just low armor - I had a Onslaught one-shot as well. Is this intended? Seems pretty odd for a destroyer to be able to one-shot S-modded-up capitals at zero flux.
Could you post your loadouts for those ships maybe?
For sure, here's one of the Paragons, and the Onslaught.
My experience is watching the Hel Hammerhead close, to within a couple hundred units (they're pretty hard to kill before they close), and then my ship suddenly explodes. There might be some system disruption being used, but the ship is lost so quickly afterward that it took a few of these events before I even noticed the shields going down. I haven't consoled in one of those ships myself, so I don't know how they function - able to shut down shields + extremely high burst damage? Even then, this Onslaught has heavy armor...