Ok, let's go through an easy one : AbilityDesignateTarget (Cielo cruiser's Designate Target ability) 
In the ability file we have:
buffInstantActionType "ApplyTargettedBuffToSelf"
instantActionTriggerType "AlwaysPerform"
buffType "BuffDesignateTargetCaster"
targetFilter
numOwnerships 1
ownership "Enemy"
numObjects 3
object "CapitalShip"
object "Frigate"
object "PlanetModule"
numConstraints 0
Note the buffInstantActionType, it applies a buff that will need targets to itself and that buff is BuffDesignateTargetCaster. The targetFilter points to enemy ships, because the overall ability targets an enemy.
So we open BuffDesignateTargetCaster:
numInstantActions 2
instantAction
buffInstantActionType "PlayPersistantAttachedEffect"
instantActionTriggerType "OnDelay"
delayTime 0.000000
effectInfo
effectAttachInfo
attachType "Ability"
abilityIndex 0
smallEffectName "Buff_DesignateTargetChanneling"
largeEffectName "Buff_DesignateTargetChanneling"
soundID ""
instantAction
buffInstantActionType "ApplyBuffToTargetNoFilterNoRange"
instantActionTriggerType "OnDelay"
delayTime 0.000000
buffType "BuffDesignateTargetOnTarget"
So this buff does two things: first it plays a graphical effect on the casting ship (that's why the ability called this buff file first) and then it applies *another* buff to the target (which you remember from the ability was any hostile ship). The second buff is BuffDesignateTargetOnTarget:
numInstantActions 1
instantAction
buffInstantActionType "PlayPersistantAttachedEffect"
instantActionTriggerType "OnDelay"
delayTime 0.000000
effectInfo
effectAttachInfo
attachType "Above"
smallEffectName "Buff_DesignateTargetOnTarget"
largeEffectName "Buff_DesignateTargetOnTargetLarge"
soundID ""
numPeriodicActions 0
numOverTimeActions 0
numEntityModifiers 1
entityModifier
buffEntityModifierType "DamageAsDamageTarget"
value
Level:0 0.250000
Level:1 0.000000
Level:2 0.000000
.. which also plays an effect on the target and makes it take 25% more damage.
So this is the general method for doing it. Your overall ability has a specific goal. In this case, the ability is cast on an enemy ship. If your self-destruct-for-big-boom case, the ability cannot be cast on another ship, because it's the ship that has the ability that needs to go boom. So for you, you can just use "ApplyBuffToSelf" since the ability isn't targetted.
Buffs are simple things. They can only affect one thing at a time. You can't have a single buff that does something to your ship and something else to an enemy ship. That's why you need two. The first buff your ability will call will self-destruct the ship and call the second buff. The second buff's job will be to do damage to all enemy ships in a radius (ApplyBuffToTargetsInRadius) which will then need its own target filter.