That seems to cheapen it, somehow. If Dark Speech becomes just a package of at-will spell-like abilities, it's hardly Dark Speech.
Were it for nearly anyone else, I'd probably agree with you ... but again, Elder Evils ... they were around when it was used in daily conversation (if you were Evil).
I'd be disappointed in my Elder Evils if they weren't fully fluent and proficient with the oldest known language of Evil. YMMV
IMO, the reason why everyone else takes damage for using the Dark Speech is because well, they don't have enough of the right qualities to be able to use it freely - the Elder Evils ought to; plus, it's a language far older than almost every being remaining in existence - the Elder Evils are among those few who aren't vastly younger than it. Along those lines, if I were to bring in the first(oldest/original) Arch-Duke of Hell, or the eldest and most powerful of the Obyrith Progenitor races, I would probably waive the ability score damage for them as well - simply because it was the language of Evil when they were young.
The actual stats of the Elder Evils are not for player knowledge/in-character knowledge. If, as DM, you make a distinction in
how you describe the Elder Evil using the Dark Speech as opposed to how the Elder Evil uses it's non-Dark Speech based abilities, then it doesn't really matter too much.
Honestly - there are abilities/effects that do basically the same thing as various functions of the Dark Speech as well or better than it - without ability score damage.
It's all in how it's presented to the players that really sets the Dark Speech apart, especially for entities such as the Elder Evils.
As you yourself said - it's not so much the abilities matter, but the flavor aspect.