Funnily, this two-parter is the only instance of the virus ever actually being mentioned or alluded to in any fashion, aside from the gag in "Trials and Tribble-ations".
And this sort of necessarily follows. After all, the point in the gag is that Julian Bashir, the medical genius with a very personal degree in Genetic Augmentation, is out like a tauntaun on the issue of smooth-foreheaded Klingons. So when ENT comes up with an "explanation", it must be an explanation nobody in-universe is subsequently aware of!
It is not within the ENT mandate to show how the knowledge of the "explanation" is lost, alas. It might in theory be within the DSC mandate, to be featured in the second season or perhaps later on. Or it might happen after the TOS era, in-universe...
Every other incarnation of Trek never plays with the idea that the Klingons ever looked different because Trek had mostly trusted its audiences to suspend their disbelief over the makeup change. The fact that the very first episode of Enterprise opened with a ridge headed Klingon basically said to me "Klingons always looked like this", and that what we saw of them in TOS was simply exclusive to that show.
Then again, Klingons always looked different in TOS already - Kor and Kang could be from different species in terms of how TOS makeup works. So it's not so much an issue of suspension of disbelief as it is one of accepting change as a constant. And specifically as regards Klingons and Tellarites, while the Vulcan, Andorian and Orion makeups did remain constant.
Certain early novels and comics took this studio feature and ran with it, turning it into an in-universe feature (multiple races of Klingons, Klingons experimenting with fusing of species to nefarious purposes, the different Tellarites being different halfbreeds). Amusingly, the studio then basically followed the lead, confirming time and again that Klingons look different from Klingons, and ultimately introducing a "reason" as well.
Personally I feel ENT for its part could also have tackled the Tellarite issue, with a different story. Their makeup is perhaps superior in quality to all of the TOS experiments, but not quite as interesting in all the details. And the Pigs in Spaaaaace! do deserve our attention - they are adorable in DSC, now with really nice tusks.
Timo Saloniemi