Taking cell phones that could be used to track your location makes no sense. And thinking that taking the phones would prevent a call being made when "Dad" has a work cell phone as well, seems like a wasted effort. This only makes sense if the "kidnapper" anticipated "Mom" waking to check on the child BEFORE "Dad" got home from work at 4am and being unable to make a call until he arrived.
It is odd that "Dad" checked the boys' room first and the missing boy did not alarm him. He did not even go to "Mom" first to check to see if he was there. Actually, with as little as we know for sure, maybe he DID, and this is why she seems so confused when she says "I woke up, we woke up" stuff... In other words, J woke D, perhaps unintentionally, looking for the son, who was in the bed with her; then went to check on the baby, waking D intentionally when Lisa was not found. So she woke twice, and her son was awakened the second time as well.
The boys are (I believe) NOT J&B's sons together, but one of each of theirs. The statements that Lisa "ties the family together" would suggest to me that she is believed to be the biological child of the two of them together. Many "stepfamilies" produce an "our child" to help unite the family.
It is possible that J was questioning Lisa's paternity (as evidenced by his comment "a woman who cheated on her husb..." and his "coldness" toward D). Lisa could have conveniently "disappeared" before paternity could be confirmed. In this case, she could have been harmed, or simply "given away" (to the baby's biological dad? A relative?) but will NOT be returned to the parents, as long as the mother also suspects the baby may not be J's.
If the relationship was in jeopardy (particularly if it hinged on the issue of paternity), D may have hidden the child (Did she have some texts at 2:30am from her brother? Who was the man at the store?) with someone she trusted to try to bring her husband closer to her through the shared tragedy, with the plan being that Lisa would be recovered unharmed and the family reunited with any prior bad feelings forgotten. This plan may have hit a snag if they are being watched closely.
ESPECIALLY if things have been rocky at home, she may realize the baby actually WAS the only thing holding the family together. If this is the case, she may attempt to become pregnant (FOR SURE by J) while Lisa is being sought; thereby producing a new "tie" between the families.
Just rambling.