Yes, I think that's more or less where they're headed. Basically different devices with different (but related) architectures, but still a shared OS, account, brand, media and some software. You could still see device exclusives depending on things like interface, play style or performance demands, but most games will run on both devices at least initially. Think of it in 3 tiers:
NX 1.0 Spec: Designed for handheld performance. Runs on as is on 2.0 devices (console) but perhaps with simple OS aided upgrades (like rendering 1080p).
NX 1.5 Spec: Designed for handheld performance but improved for console. Basically a dual sku (think MH4U) that improves shading, assets, performance, etc when it runs on the more capable 2.0 device.
NX 2.0 Spec: Designed for console performance. Incompatible with NX 1.0 devices.
Then you still have semi-distinct platforms that can appeal to different core bases/regions without sacrificing much, but you also reduce risk by sharing software across devices and potentially avoid the pitfalls Nintendo's current consoles face with content starvation. Even better the next handheld several years down the line could be built to "NX 2.0 Spec" and then immediately have a giant library, full backwards compatibility, developer familiarity and an already invested userbase. Then you keep the cycle going with a 3.0 Spec console, and soon NX is looking more like iOS or Anroid and less like what we have now in terms of console generations and transitions. I really feel like NX has to be this sort of huge break from the current model and shift the idea of what a game platform is, it really can't just be another closed box with an interface gimmick grafted on top.