My gut is telling me that the VSD will not go extinct. Yes the ISD can do everything a lone VSD can do, only better. However the points difference will still keep the VSD a very solid choice in many lists. Want to include a dangerous area-denial ship in your list? 120+mods for an ISD is a heck of a lot of points to sink into that. 73+mods for the VSD-1 is a much more reasonable alternative.
Also, once you get over the monstrous front arc firepower on the ISD, it's not so superior to the VSD. I would even argue that the 2 reds in the rear of the VSD may be superior to the 1 red and 2 blue that the ISD gets.
Defensively, the ISD has a major advantage with a total of 5 extra health. It also gets that nifty contain defence token that will help preserve it from critical hits, but not from any other nifty card-based critical effects. Other than that the ISD has the same defence tokens as the VSD. Importantly as well, both the VSD and ISD have 4 engineering, so both ships recover from damage taken equally well.
Manoeuvrability wise, yes she is much better on paper than the VSD. Once ships and obstacles start getting in the way of that big base however, we might find her to be less manoeuvrable or easily predictable. With the size of the base it will make getting double arc shots against the ISD quite easy mitigating the ISD's health advantage to a certain degree.