There is a circuit in the battery to protect it from being totally destroyed, and there's also something in the N800 to switch it off before you get that deep down. Still, depleting the battery isn't good. Even a single deep discharge can damage it. I once let my phone run for three weeks without charging (switched off at night though) because the connector was broken. After that it needs recharging every second day.

My N800 battery seems to be doing well after 9 months. I normally charge it whenever I see it drop down one or two bars, although it's happened two or three times that it discharged during the night (until I disabled a certain crawler program..).