Not always. A direct flight that departs at 6am or lands at midnight can be harder than a one-stop routing with a civilized departure time and a 4-hour connection at a hub with a quiet space. Compare the whole travel day, not just the time in the air.
Not always, and this is the assumption worth testing first. A direct flight removes one transition, which matters. But a 6:10am departure is not really an early flight. It is a 3:30am wake-up, a dark car, an empty terminal, and a security queue before breakfast. Landing at 11:45pm in an unfamiliar city costs you the next day too.
Set the constraint by the day rather than by the number of flights. Something like "nothing departing before 10am, nothing landing after 8pm" is a real routing constraint a consultant can build against, and on a multi-stop fare it usually costs less than people expect.
Overnight long-haul cuts both ways and there is no general answer. The cabin is darker, quieter and less crowded, which some children handle far better than a bright, full daytime cabin. Others lose the sleep routine and pay for it for three days.
Compare the whole travel day, door to door, including the transfer at the far end. A one-stop routing through a hub with a bookable quiet room and a 4-hour connection is often the gentler trip even though it looks worse in a search result.