Bethesda faced a similar problem when making The Elder Scrolls IV: Oblivion. They considered adding children to make the game more realistic, but this was a controversial choice: if the children could be killed, Bethesda could be accused of making a child murder simulation. Bethesda's response was to simply make the characters invincible. This once again raised issues, because the tactic would undermine the purpose of adding children in the first place, namely, realism. Eventually, Bethesda scrapped the idea for The Elder Scrolls IV: Oblivion, but in Fallout 3 they went the other way, allowing children for authenticity, but making them invincible.
Timmy Neusbaum of Tranquility Lane is removed when the task to slaughter the residents arises, or when the Chinese invasion program starts. A unique Garden Gnome called "Timmy the Gnome" is placed on the Neusbaum doorstep, indicating that Timmy's Tranquility avatar has been altered. After the Lone Wanderer leaves the simulation (after using the failsafe), examining Timmy's vitals verifies his death.
Children cannot be targeted in V.A.T.S. However, if they are accidentally injured, they can sustain crippled limbs.
Since children cannot be harmed, they will generally not fight the player character, even if they are armed. Instead, if attacked, they will flee.