This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
Sonia was not originally meant to be Irene Lew, but a replacement for her, in the same way that the new Ninja Gaiden 2's seems to be a replacement for the original Ninja Gaiden storywise. However, with Itagaki gone, Team Ninja now wants the new games (as well as DOA) to have continuity with the old ones, hence the Retcon of "Sonia" simply being a codename for Irene.
Possibly, but Itagaki did tease the fans prior the official release of Ninja Gaiden II (Xbox360) that Sonia might not be her real name, and many years before that, when Itagaki created the Dead or Alive franchise, he was the one who accepted Ryu as a Guest Fighter in his game and started the merge the series in the first place; it was in the first Dead or Alive game that the fact Irene and Ryu married became Canon Immigrant from the OVA. Itagaki only started his Flip Flop of God after the 3rd Dead or Alive or so; things started to merge togther more after his leave from Team Ninja, but Itagaki did start The Verse thing, and eventually would merge things out his way had he stayed, so it's not just new Team Ninja's idea.
One of the paths for Itagaki's possible plans to merge the Ninja Gaiden and Dead or Alive worlds was through Muramasa change of jobs. The last Dead or Alive game by Itagaki was the 4th one, in it there's a stage with Muramasa running a Vegetable Mart; something which he never mentioned to have in the Ninja Gaiden time-line. There might be a connection to Ryu's ownership of a Antique Shop in Dead or Alive and Muramasa's rennouncement of his own for a Vegetable Mart, it could be a Re Tool in that Muramasa passed his Antique Shop to Ryu as he went on to open a more healthy business; the Original Video Animation never actually explained how Ryu opened the shop, and the Re Tool can just discart or expand the fact that originally the shop resides in America, Dead or Alive don't actually says where Ryu's shop is located, and Muramasa appears to have more than one shop, so Ryu's shop in america could be just another one of Muramasa's.
Should the NES games be redone, they would likely be based on the New series but traits/signs from the original games (such as the shadow clone and sword extend power ups from the later NES games)