I always had the idea that Irenicus discovered Imoen's Bhaalspawn identity during her period of captivity, perhaps while performing the long hours of experiments and torture upon her and the PC.
Probably the best bet since it wasn't really explained.
I guess I'm looking at it this way:
In ToB they make mention of Gorion snatching you from basically the nursery of Hell where they'd gathered all the Bhaalspawn babies in some attempt to resurrect Bhaal. IIRC, they were going to start sacrificing babies shortly, but Gorion and company came in and stole the pc.
Now obviously, lots of Bhaalspawn survived so it's possible that Imoen found her way to Candlekeep by other means. Jaheria says that Gorion was part of their adventuring party prior to settling in Candlekeep, which leads me to believe that she was part of the Bhaalspawn kidnapping.
So how does Imoen end up at Candlekeep? If it's not in the same snatching as the PC, it seems like a big coincidence that she would end up at the same location, roughly at the same time, and no one would take notice (were there other kids around? I always got the impression that Imoen and the pc were the only youngins there).
That's where I make the leap to thinking Gorion had to know and if he knew, Jaheria must know as well.
Either way, it's not like it hurt my enjoyment of the game. It just seemed like a bit of a cop out. I guess they needed a character to be the Bhaalsibling that you would actually want to go after and rescue, but it could have been interesting to make it another character with a separate backstory you had to figure out. (Hmmm, maybe a good mod could be made on that!)