I think that's the games own balance.
I guess you are new, i'll try to explain as clearly as possible.
There is essentially 2 different types of damages in game. Standart and Armor piercing.
Spell damages are not different. For example lets imagine a vortex spell just like bladewind. It's stats would be something like 17 standart 3 AP damage per second.
Bladewind's standart damage is exceptionally high, especially when overcast. It, however, has very very low AP damage value. It is, at the top of my head, something like 23 standart and 0 AP damage when not overcast and 23 standart 6 ap damage when overcast. (or somewhere along those lines. cant remember RN you have to check the game logs.)
Yes the bladewind is potent against archers, but it falls of very sharply against armored units. These Malekith vs Entire armies thing is very normal especially if you allow enemy Legendary Lords to level up too fast in the early game. They start to decimate entire armies by themselves becasue early-mid game units don't have answers to them.

""""""Another thing is, Spell damages and area effects DO NOT CHANGE with unit sizes. Meaning, if you are playing on Low or Med unit sizes, a damaging spell will do SOO much more damage relative to your army size. E.g. with Small unit sizes, a unit of archers have 24 models (i guess.) whereas in ultra size, they have 90. A bladewind will strait up decimate 24 units before you can react whereas an ultra sized unit might lose 15-20 models or so before you can react and reposition them."""""""""""""""""""

Your best bet is a Light Wizard with sisters of Avelorn spam. Net him and get him from afar. Focus fire from 5-6 Sisters should melt any Lord within 30 seconds.
Don't worry they are supposed to be that powerful.

Malekith is very powerfull, usually i use a light wizard to web him (and his dragon) and gunpower units to open a lot of new holes on him before he can get free.