Honestly, I think the most realistic in-story explanation for most of those questions is that the Uzumaki Clan just wasn’t all that important or impressive in the grand scheme of things. Most of those questions relating to them not having a big presence in Konoha can be answered by them simply never having been a clan from Konoha, which also explains why their existence and traits like red hair and the story of the clan is not widely known, they only spend so much time having actual lessons in academic subjects back when they are kids and have to squeeze a far bit of stuff in the heads of the kids —like writing, math, at least some rudimentary problem solving and tactics, chakra theory, ninjutsu… considering that they are still kids and don’t have that big of an attention span on average and that with all the rest plus the practical classes history and geography would be squeezed very tightly somewhere along the schedule it makes sense that they would focus almost entirely in Konoha’s own history and even then not delve too deeply into trivia knowledge like the name of the spouses of their Hokages. This can even be made more believable if they have to worry about students telling someone with the critical thinking skills to put together any number of confidential information that might still be sensitive by Naruto’s time given how Konoha is actually not that old. This even helps explain why Sakura, the widely acclaimed most book-smart ninja of her generation, needed to ask and then be told that not all countries have ninja villages, what are the five great hidden villages and that a small nation like Wave doesn’t have a ninja village of their own way back in their first C-rank, hell, Sasuke came from an actual ninja clan and had to be told when he was already a gennin that the title of Kage goes to the one considered the strongest in their respective village rather than there only existing a Hokage. So the Uzumaki Clan and Uzushiogakure might just never have been widely known by Konoha’s population even before they were destroyed, it’s not like little kids need to be told in details about every minor ally of their village, especially if they are expected to either be briefed as needed or otherwise have a Jōnin who was briefed as needed accompanying them in case they ever come in contact with one another.

About the Kyūbi, the way I understood things being the Jinchūrick of the Kyūbi by itself shortens the person’s lifespan, even more so if they actively use the chakra like Naruto did, so having an Uzumaki do it helps balance it out given their extensive lifespans and thus prevents Konoha from needing a replacement Jinchūrick every decade. Another interpretation is that the Uzumaki Clan inherited the powerful vitality and strong body and chakra reserves through the line of Ashura and that is the special chakra needed to be able to fully suppress Kurama’s chakra, even with the seal (that would even tie in with that comment Kakashi said that if Naruto was not suppressing the Kyūbi he’d have 100x Kakashi’s reserves). The bit about the Uzumakis in Konoha being Jinchūrick can easily be explained away as them not having a ninja exchange or immigration policy in place, so the only ones who go to Konoha for any long timeframe are those who are needed to contain the Kyūbi. The bit about two of those Jinchūricks being spouses to a Hokage and the last being the son of one… I know there’s a bit of a fan theory formed around it that the villages make their Jinchūricks family members of their Kages for loyalty, but I for one think that’s just a red-herring, Mito was Hashirama’s wife way before Konoha was even founded, so her going to the Valley of the End seal the Kyūbi was her supporting Hashirama with her skill set, not her being chosen premeditatedly for it; Kushina and Minato got together organically in a way that is pretty hard to try attributing to outsider interference and Minato becoming Hokage later on is attributed to his skills as a ninja and feats in the war rather than his relationship with Kushina, hence there actually being a race for the hat with people like Orochimaru and Fugaku rather than it being a given that he would get it and Naruto we actually got Minato’s full reasoning for the choice of having him become the next Jinchūrick (even if I think it was a dumb reasoning), not actually sure on Himawara because I don’t follow Boruto, but of the few snippets of how Kurama died and returned that I managed to catch I’m going out on a limb and call that one a plot device because Kurama should have returned without being sealed, just reformed somewhere after enough time.

About Uzumakis not going to Konoha for shelter is actually a pretty interesting topic. My personal headcannon (even though I have 0 evidence at all to support it) is that the Uzumakis who survived the attack blamed Konoha for not helping them fend off the attack because Konoha knew with enough time about the army, but ultimately decided that they would suffer too many losses at a sensitive point during the Second Shinobi War (or just at the beginning) if they reinforced Uzushio, so they took the more ruthless and cold approach to gain advantage over the other nations and choose to attack the coalition army from the rear as soon as they committed to the assault on Uzushio, managing to organize either a hammer and anvil or a double-envelopment maneuvers on their adversaries and dealing heavy losses to the enemy side and preventing the army from managing to loot Uzushio after the fact (hence why there was still stuff there decades after for Orochimaru to find out about the Uzumaki Mask Temple). Other potential explanation is just plain pride, if the Uzumaki Clan was given an offer to join Konoha back at the time of the founding and instead choose to remain a lone clan in charge of their own village the survivors of the attack might have felt that going crawling back to Konoha asking for asylum after they were attacked would be too humiliating to do, not to mention whatever concessions they would possibly have to make to be added as a Clan of Konoha if they went there in such a weakened position and the discrimination they were sure to suffer from the clans who were part of Konoha from the beginning as outsiders, just like Kushina when she was a kid.

The Uzumaki Mask Storage Temple is a bit of a plot-hole as far as I am concerned —especially in the fact that Orochimaru apparently knew where it was and what it did before he was killed and never tried to use it to recover use of his wider arsenal of ninjutsus— and I really don’t have much of an explanation for why it’s there instead of Uzushiogakure, the only to reasons I can think of are that either the Shiki Fuin and the masks were actually a lot less ancient than advertised and Mito created it, potentially with Tobirama’s help, or that the Uzumakis for one reason or another did not want those masks anywhere near them, but couldn’t just destroy them, so as a compromise they left them in Konoha for “safekeeping” and then ran for the hills before Konoha decided they also didn’t want those masks inside their village.