Resurrecting for current data point: I signed up for NAB's current Qantas Signature offer in late November. I've received two statements since (one just 2 weeks after activating the card, the second this week) and today realised the points from those two statements never did come into my QF account, but are listed correctly on the statement. I've also just crossed the spend threshold for the first tranche of 90K bonus points.
I received an e-mail last month reminding me of the 90K offer if I hit the minimum spend and I see both my name and QF number are correctly listed on that reminder, but from a quick search here and elsewhere, it seems that this doesn't necessarily mean the accounts are properly linked and that this is an ongoing issue.
It seems that may still be the case, so I'll call NAB tomorrow and report back.