To the best of my knowledge the (in-universe) explanation for why the Klingons didn't have cranial ridges in TOS was because of a genetic disease caused by attempts to manipulate Klingon DNA to create augments (like Khan):
In the year 2154, the Klingons gained access to the genetic material of Human Augments and tried to adapt this genetic engineering to improve themselves.... One of the subjects suffered from the Levodian flu, which was modified by the Augment DNA to become a fatal, airborne, mutagenic plague that spread rampantly through the Empire, from world to world. In the first stage of this plague, Klingons lost the ridges on their foreheads
However, I recall seeing in the episode chain of Enterprise where the Klingons became infected with the virus, that the augmented children that the Klingons based their research on were augments from Khan's folk.
The scientist who leads the augments is Dr. Arik Soong (an ancestor of Dr. Noonian Soong, Data's father). Now if these children were augments then, in the prime timeline, Dr. Arik Soong likely found them aboard the Botany Bay and took them for safe keeping. However in the Abramsverse the Augments are likely under section 31's control and so would be kept under guard on earth, meaning that the Klingons wouldn't experiment with genetic research. Therefore everything is fine then? No.
Because the Augment virus ravaged the Klingon population prior to the U.S.S Kelvin's fateful encounter with Nero, then the Klingons (or the majority of them) should still have disease-ravaged heads in Into Darkness.
So how/why exactly do the Klingons in Into Darkness have cranial ridges?
Answer
Many millions — but not all — of Klingons were infected by the augment virus (ENT "Divergence"), and so a reasonable (but unconfirmed) in-universe theory would be that the Klingons in Into Darkness were descendants of those who were not infected.
ANTAAK: I suppose this is what I deserve. Millions of my people will have to live with this disfigurement. It'll be passed on to our children. Life won't be easy for us.
The words of the Klingon scientist Antaak imply that not everyone was infected. Also, we should take into account that we had never seen Qo'noS in TOS. The Klingons in Into Darkness were encountered on the homeworld itself, where one expects to find a greater diversity of Klingons.
All of that being said, one of the film's writers, Bob Orci, used to frequent the TrekMovie news site (before he famously lost his cool with Star Trek fans). In the lead-up to Into Darkness, he said
- boborci - June 3, 2012
So in our universe, they still have ridges, whether they are in the sequel or not;)
(Source)
I interpret this as saying that they were explicitly retconning ridge-less Klingons from TOS and the genetic augment virus from Enterprise.
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