Summary: Jack is considering all that needs to be considered
It had all started sometime after Sha're died. Daniel needed someone to hold on to, someone to tell him he still had enough to live for, someone who showed him that, in his thirties as he was then, the best part of his life wasn't already over.
Jack was the one there for Daniel. Though it took him a while to know for sure that he wasn't taking advantage of Daniel.
Now, these years later, a decision would soon truly be upon them. Did they bring up their child in either their Stargate World, their newer, to them, Warehouse 13 world, or the outside world where he and Daniel would hav to pretend aliens and artefacts didn't exist, all the time, waiting for them to fall out of the sky, and/or cluster around their feet! Could they wait for when they might be needed by either secret organisation, meanwhile trying to give their child a normal life?? Thing is, Jack knew the dangers of bringing up your child in the world you, the parent, was used to. However many times Daniel told him it wasn't, Jack counted Charlie's death as being his fault. Jack didn't want his new son to pay any price... So, what to do? Jack thought back to the way Daniel felt when they first got together. He knew how horrendous pain and loss of hope like that was.
Each other, and now, their new child, the new family unit for both of them, were Jack and Daniel's hope. Jack didn't want to risk that for any of them...