No, it does not matter, if you use the touchscreen to swipe pages or the side buttons. I tried it with 100 page swipes in a row. Both used the same amount of battery.
I have no problem with battery life at all. I think it last pretty long, as long as you just read on your Nook and don't play around with the touchscreen all the time. Which is of course very tempting in the beginning
My setting is flightmode off and wifi on all the time and it last a long time this way Cannot complain about that.