Would you say it throws up red flags on Blizzard's side if you're running two WoW licenses simultaneously on one bnet account?
No
It is too common for multiple people to play under the same account. If a parent and child both play then they would likely play under the same account because someone under the age of 18 cannot legally be bound by the EULA. Someone under 18 is supposed to play under a parent/guardians supervision.
Also, with the introduction of account wide achievements many families play under the same account to share these achievements. You've got to remember that there are entire households that play wow together. There could be 5+ people logged into the same account using the same IP address at one time, and that occurs on a daily basis under completely legitimate circumstances that does not involve botting.
It is my opinion that there are two ways to get banned by Blizzard:
#1 Someone reports you and a GM investigates. If you are reported and invested then they likely have enough information to tell if you are botting on or not.
#2 You get too extreme with your botting. 100+ accounts from the same IP, mailing 1 million gold a day for over a week, or some other activity that not be normal would be the likely triggers. The criteria for investigating someone that was not reported would have to be enough to make the percentage of people very small. If the criteria were not extreme then too many people would show up in the list, and they would not be able to investigate them all.
In short, if you are a normal gamer then the only thing you likely have to worry about is someone reporting you. The only people that should be concerned about getting flagged are those that are trying to make money off of the game through gold selling, item selling, account selling, powerleveling services, or anything else that requires running a lot of bots. You make very little money from in-game sales for RL money, so in order to make any decent money off of it you have to do a lot of it.