We know that there are 3 Zechariahs involved in the Tisha B'Av story
1. is the Tanna Rav Zechariah Bar Avkulas who did not let the Chachomim allow the Roman Emperor's Korbon be brought in the story of Kamtza and Bar Kamtza in Gittin Daf 56 where Rav Yochanon comments that the Anvenusoh of Rav Zechariah Bar Avkulas lead to the Churban
2. Zechariah no 2 is the Kohein and Novi whose blood did not stop bubbling after he was killed in the Azoroh when the Yidden had enough of him . He is Ben Yehoyodo and his name only comes fleetingly in Divrei Hayomim Beys but the story is brought about a dozen times in the Medroshim and Kinnos mentioning how many Aveiros were involved by killing him.
3. The last one is Zechariah Ben Berechyah the second last of the Trei Osor whose Nevuah is referred to in the famous story of Rabbi Akiva and his fellow Tannoim at the end of Maseches Makkos.
I cant understand why in the list of the 48 Neviim in Megilah Daf 14a that Rashi lists he only gets to 46 and does not know who the other 2 are and in his list he only brings Zechariah Ben Berechya NOT Zechariah Ben Yehoyada and what is more Shvare a) the RACH in his list on the Omud Beys of that Sugya does bring him down and Stam an extra Kasha why does the RACH list the Sheva Nevios what is he adding they are written Mefurash in the Gemoro on Daf 14a and b) the Rambam in his Hakdomoh to Yad HaChazokoh when he goes through each Dor of the Mesoirah lists both Yehoyodo and Zechariah so they are Neviim part of the Mesioirah so by me that Rashi is Tzorich Iyun
Boruch Kahan
Lonfon England
Rashi is following the view that a Navi is mentioned only if his Nevu'ah was required for future generations. Despite the prominent mention of Zecharyah ben Yehoyada in Kinos, there are no known Nevu'os from him for future generations. This does not contradict him being part of the Mesorah, as he could transmit Torah without transmitting Nevu'ah, just as the Shoftim did.
That said, there are other controversial choices in this Rashi which are disputed by other Rishonim, such as Rabeinu Chananel and the Rambam, as you rightly mentioned. Neriyah, Machseyah, and even the Avos are disputed by others. The Vilna Gaon says that the two missing Nevi'im are Chanani and Oded.
Rach mentions all of the Nevi'im, so he also mentions the Nevi'os.
Yoel Domb
Shkoyach
So what in fact is even more difficult to understand is why the killing of Zechariah made such a Kitrug in Shomayim that caused Nevuzaradon to kill so many Yidden,I think the fact that Zechariah was a Novi is a side issue the Ikar was that he was killed in the Azarah by the Yidden on Shabbos Yom Kippur and that KLAL YISROEL WERE SO UPSET BY HIS WORDS OF TOICHECHOH THAT THEY DID THE ULITMATE AVEIROH OF ACTUALLY KILLING HIM.
I was further thinking that we famously know the Gemoro in Yoma Daf 9 that the reason why the FIRST Beys Hamikdosh was destroyed was because of the 3 Aveiros and perhaps the Medroshim/Kinnos wanted to highlight at least 2 of them in this story that being Shefichas Domim and Avoidah Zoroh because if you go through the Kinnos and Medroshim there seems to be much more of a focus on the Sinas Chinnom which caused Churban Bayis Sheni and we are hardly told of Giluy Aroyos being one of the 3 reasons of Churban Bayis Rishon . There are some references in Sefer Melochim Beys to some of the forbidden marriages that Malchei Yehuda did but somehow the story of Zechariah is very prominent focussing on the other 2 Aveiros.
Finally the whole point of my shtikel and Heoroh was to point out the common mistake that even Rabbonim (I know since I asked a few of them who live in my Kehilla) make when they always refer to Zechariah HaNovi being Zechariah Ben Yehoyodoh and assume he is the Zechariah Ben Berechyah of the Trei Osor and I personally would refer to him more as Zechariah HaKoihen.
Boruch Kahan
Regarding your first point, I think the fact that he was a Navi also contributed to their punishment, as it says in Eichah. This was a holy person in a holy place on a holy day, and it caused a tremendous Chilul Hash-m which can be atoned for only by death.
In Divrei ha'Yamim II (24:22) we find that his last words were, "May Hash-m see and avenge," implying that he wanted a Nekamah from Hash-m for his death. This could be the reason for the severe punishment meted out to Am Yisrael, since there was no protest over this act and therefore everyone was held responsible for it.
As for your second point, the Nevi'im do speak extensively about Giluy Arayos (see, for example, Yeshayahu 3:16, Amos 2:7, and Hoshea 4:2 as explained in Kidushin 13a, as well as various other sources). The Kinos do focus on this as they explain why women were raped during the Churban, since they practiced Giluy Arayos beforehand (this is in the first Kinah I believe).
You are correct that there was more than one Navi called Zecharyah and people can confuse the two. It only emphasizes how important it is that a Talmid Chacham should know all 24 books of Tanach (see Rashi Shemos 31:18).
Yoel Domb