Gravity anomalies surveys are used to understand the nature of the crustal material. Positive anomalies, or higher gravity than surroundings suggests higher density (heavier) material, (iron, metallic composition) where lower some lighter alternatives.
A good example of this is the Chicxulub impact. The map of gravity anomalies show the crater quite clearly, even if it is buried under thick layers of sea sediments or surface (Yucatan, MX).
On the other hand, Nastapoka arc is harder to define using similar methods. This recent paper (PDF) (now published here) discusses that it may have more to do with crustal dynamics than an impact. Nevertheless they present an interesting gravity map of the site (See figure), where any links to an impact in this area would not be obvious.
It is true that major glacial activity occurred repeatedly during the Pleistocene east of the Hudson Bay (eg: Laurentidian Ice Sheet sweeping again and again), but yet the Chicxulub impact was subject to many factors of erosion as well since its formation near the K-T boundary.
Still these kind of surveys indicate the nature of the material in the crust - so even if several glaciations impacted the Nastapoka arc area, there would be some kind of patterns still present indicating heavy metals (Chondrite or anything typical of an impact, iron or circular metamorphism).
To conclude, unless other surveys suggests an alternative interpretation path in the future, few evidences strongly support the theory of an ancient impact at Nastapoka.