Firstly, is this a coverup? Perhaps Rav Huna actually meant "day," and is simply wrong, or meant "day" and was correct, in either case basing himself on sources implying that or meant day? Just because we "prove" that Or in the Mishna means night does not necessarily entail both Amoraim being correct. On occassion, in case of dispute, an Amora is found to be wrong.
Perhaps one might answer that here, because Or meaning night is so obvious (since the third Mishna uses Or Arba'a Asar as opposed to the later Arba'a Asar Shacharit), one could not imagine that Rav Huna got this wrong.
On the other hand, it would help is there was some independent evidence that naghei can mean night.
Indeed, we find this evidence in the statement of Abaye. On Pesachim 4a, we have:
אמר אביי הילכך האי צורבא מרבנן לא לפתח בעידניה באורתא דתליסר דנגהי ארבסר דלמא משכא ליה שמעתיה ואתי לאימנועי ממצוה
There seems to be a distinction between oreta and naghei, such that one belongs to the 13th and the other to the 14th, which is worthy of discussion in a separate post. (Which might mean a major difference between the girsa of Or Arba'a Asar vs. Or leArba'a Asar, and furthermore might turn the Rav Huna and Rav Yehuda into actual disputants! But this is for the separate post.)
But see! Abaye uses naghei specifically to mean the night of the 14th - that is, since Hebrew calendar days begin at night, the night of the 14th is the naghei of the 14th. Rashi helpfully translates this as the leil of the 14th.
So there is no coverup.
However. And it is a big however.
There seems to be a major problem saying mar ki atrei umar ki atrei, that each spoke based on the language of his place.
First, as I advanced in the previous post, Rav Yehuda is not just explaining it using the language of his place, but is echoing the words of the academy of Shmuel. Since each learned under Shmuel, it is likely that they are both repeating his explanation. Indeed, the academy at Pumpedita, founded by Rav Yosef, was a replacement for Shmuel's academy at Nehardea, which was destroyed, and thus this a continuation of the tradition.
Second, and most importantly, we must know a bit about these people and where they live. Many of these were the heads of academies.
Abaye, who said naghei, was the Rosh Yeshiva of Pumpedita.
Rav Yehuda, who said leilei, founded the yeshiva of Pumpedita. Though two years prior to his death, he headed both Sura and Pumpedita.
The academy of Shmuel, which said leilei, was in Nehardea.
Rav Huna, who said naghei, succeeded Rav as the Resh Mesivta at Sura. (Rav had founded this.)
If this was all a dialectal difference based on location, then Abaye contradicts Rav Yehuda. Both were in Pumpedita, yet one said leilei and one said naghei.
Perhaps one can say that it is not based on the dialect where they were when they said it, but based on the dialect with which they grew up, which makes more sense. However, I am not sure if we have this sort of information available.
Alternatively, we might say that in Nehardea they said leilei, while in both Sura and Pumpedita they said leilei. Rav Yehuda, as founder of Pumpedita, was continuing the tradition of the academy at Nehardea, and thus says leilei, while Abaye, operating a bit later, uses the local dialect.