There are two different types of deceit in I Am the Cheese. First we have explicit deceit, obvious to both the characters and the readers: Adam's parents lied to him about their past. More captivating, however, are the subtle manipulations that we can't really be sure of. The fact that Adam doesn't know if Brint is lying to him (and for that matter, if Mr. Grey was lying to his family) creates a sense of suspicion that wouldn't be there if the lies were out in the open. Explicit deceit leads to a feeling of betrayal and isolation; subtle and manipulative deceit leads to paranoia.
Adam is lying to Brint more than Brint is lying to Adam.
Any lie is a betrayal. Adam's parents were not protecting him by lying about their past.