Some enemy units can be too costly to engage with ranged units and infantry and this is when the scout bomb is invaluable.
The basic concept behind the scout bomb is this, scouts travel so fast they reach the enemy troops in one round before the enemy has the chance to attack them. They target the units with the highest value, and their real use is taking out powerful units like ballista. However they can be easily defended against. While large scout bombs will decimate ballista, if they hit other units like swordsmen they will cause very minor damage.
When you really want to use them is when say your enemy has 300,00 archers, swordsmen and ballista. In this case the scout bombs will hit the ballista because they have the highest attack value. Because ballista have very low defence value they should take out a large number of them, around 5,000 to 10,000 with a 100,000 scout bomb. But lets say the enemy has 2,000,000 swordsmen, 1,000,000 archers and 300,000 ballista. In this case the scout bombs will hit the swordsmen and only kill about 1,000 or 2,000 if even that. This is a very small number to kill and if you do the maths scout bombs are not viable to use to clear out infantry. If the archers had the highest attack value, you could expect to kill between 10,000 and 20,000 even if the enemy has a few million, because archers have a very low defence value. They can be used to clear archers because if you have raised the enemies honour high enough you can keep scout bombing them getting good heal rates and kill a few 100,000 softening them up for mech waves.
Small Scout bombs can also be used to spam out enemy traps.
If its a case where your city has been wiped down to just a large number of say ballista, you might as well try to avoid being scout bombed by closing your gates. The best defence really against scout bombs is to keep a large amount of swordsmen and pikemen in your city. That way the scout bombs will hit them causing very minor damage.