I don't think it's possible to void warranty for N900 (unless you want to change product code and IMEI)

Flashing firmware is ok.
Flashing to another firmware is ok.

It's like a computer, you get it from a shop, it comes with Windows, getting rid of it and put Linux on. When it's broken (hardware wise), you do factory software restore and take it to the shop to fix. There are no way they can tell what you've been doing with it.

I am aware NSU sends all sort of data about the phone to Nokia.
If you are afraid, just use the flasher too and avoid NSU