Hiding Peter was not intentional; in fact the decision was never vocalized. However, it became a necessary after Tony finally got Peter’s medical records and found some oddities.
Peter was born three months before his due date. He was less than a pound and five inches. And blind with possible deafness.
The records end there until a year later where Peter is noted as a healthy, normal baby with near sightedness and asthma. The rest are marked classified, until Peter is under Ben Parker’s care.
Tony knows this is something SHIELD or whatever they call themselves would want to know (probably already have a file) and he shows it to Steve.
Nothing is said, but after the first few months, they do not mention Peter to anyone, which is hard when that includes spies, a Norse God, a guy with wings, a Hulk who
with them, and Agent Coulson’s pitiful look when he sees them.
Read the rest via the link in the description!