It's foolish if QF ignores BNE.
BNE-NRT was a very popular route. When JL was flying 747, it was always full. It was dropped mainly because JL went into bankruptcy not because of lack of demand.
OOL-NRT can't fulfil that demand. Getting to OOL from BNE is so inconvenient. There is no public transport and if you don't have a car or on one can pick you up, the only way is by private shuttles or taxi. Private shuttles only pick up people at ridiculously early hours (like 5am) in some designated spots in Brisbane and they don't service everyday. So if you need to depart or arrive on one of the days they don't service, taxi is your only option. It costs $200-300 rt on taxi, which negates any savings you have with JQ.
As a result, many Brisbanites would rather transit somewhere else. Unfortunately transiting in SYD is so inconvenient as it requires you to pick up your luggage and change terminal and then drop off your bags again! During summer, BNE is 1hr behind SYD, so to connect QF21 that departs at 20:30, you have to leave BNE at 16:00 at the latest, this many people who work very hard to leave on Fri after work.
So, many have gone with SQ or CX (and CI/BR to some extend) as they have late night departure flights (easy to go after work) and transit in SIN/HKG/TPE is seamless.
If QF would start BNE-TYO direct flight (whether NRT or HND, JQ or QF), I'm sure there will be lots of demand. If QF is concerned, maybe consider 3x/week BNE-HND, and 4x/week MEL-HND to fill up the 7 days slot and see how it goes.