I haven't updated the device through NSU. It might be specific NSU issues. I encourage you to file bugzilla to give stronger feedback to Maemo team.

Flasher might be the safest way (from my experience) since you are going to develop some apps on Maemo. I have flashed my devices hundreds times with flasher, not a single failure yet.

Sorry I couldn't provide experience from Windows perspective because I don't have Windows at all. :-/