For multiple bolt/blast/ray spells, you should resolve the attack for the first blast/ray/whatever before declaring the target of the next.
Magic missile specifically says "The darts all strike simultaneously", which defines the normal behaviour for spells such as
eldritch blast and
scorching ray to be striking sequentially. Additionally, Crawford's tweet about repelling blast pushing a target out of range of further bolts lends weight to the sequential behaviour.
An archer with Extra Attack (level 10) can shoot 3 arrows, at one, two or three targets. All 3 attacks have DEX added to the damage. The attacks are made sequentially by the player (e.g. if the first arrow kills the first target, the archer doesn't have to waste any more arrows on a downed foe).
I'm also fine with adding the CHA/Elemental/whatever damage bonus to each ray. regardless of the number of targets, though the errata specifies that this is not the case for Draconic Sorcerer elemental affinity.
Since there is a chance of a miss, adding the CHA modifier to each bolt, even if multiple bolts hit the same target, seems fair to me. After all, the archer gets to add their DEX mod 3 times to damage, even if all 3 arrows hit the same target.
Area of effect spells are different. In that case, there is no attack roll because all targets in range get automatically hit (with a saving throw to reduce or negate damage). In that case, the ability score modifier gets added once to the damage value that applies to everyone.
Still think EB is over powered.
If you compare it to a magic longbow or crossbow, it's not quite as powerful as it seems. Still powerful, but then again, it is the primary ranged attack of a warlock.