No, BN3 is your sequence number (i.e. you were the third passenger checked in to your flight.). You should've seen the seat map when you performed the checkin and allowed to select your seat. If you didn't, something fishy was going on. Do you actually get assigned seating on Danish domestic flights?

Anyway, just go to the gate (if security gives you any trouble about a missing boarding pass, just show your printed confirmation) and tell them that you checked in online and they will print your boarding pass(es) to you. They'll probably want to see either your Eurobonus card or the confirmation.

Have fun.