Who says Bob never spotted Bonnie growing? Who's to say that Mab didn't visit Bob and specifically threaten Bob to stay quiet? And before anyone says that Mab cannot cross over Harry's threshold, Harry has been in her debt from before Harry picked up Lasciel's coin. Mab can go where she wants and do what she wants. That's why she was able to take Harry's boomstick in Small Favor.
There is no indication that Bob is fae. He is able to lie as well as evade, misdirect and intentionally misinterpret questions. So long as Harry never directly asked "Hey Bob, do you see an entity that is technically my offspring growing in my skull?", Bob could argue he never lied. Heck, are we even sure that Mab is really after Bob? The only reason why we know that Mab wants to find Bob is because Bob said so. For all we know, Bob could be a mole under the control of Leanansidhe (and thus Mab) when Lea helped Harry defeat DuMorne. Remember, we only know what Harry knows.
The fact that Bob asked for a backup skull right around the time when Bonea would need a place of her own to occupy is highly suspect and way too much of a coincidence. In my opinion, this is an example of Bob helping Harry (and maybe passively resisting Mab's instructions) without Harry being aware of it.
