1. There's no proof against it either
2. Inventions get lost, for example Nikola Tesla was the first to find something to make electricity inexpensive yet Thomas Eddison gets the credit. Eli Whitney invented the cotton gin but do you know how many people tried to lay claim to this and succeeded? They orobably never heard of him eother there's no document back in that time for who invented what. Unless it's legendary
3. That's an opinion there are already character sketches of the filler characters
4. Ninshu and ninjutsu are basically the same thing. So you can accept that hagoromo using creation of all things is ninjutsu but you're going to say ninjutsu didn't exist? Heck Hagoromo's rinnegan techniques are ninjutsu. The difference between ninshu and ninjutsu is that ninjutsu is internalizing chakra and weaponizing it and ninshu is the sharing of that chakra. In other words anyone can internalize chakra and weaponize it but Hagoromo as a traveling sage did not believe in such things. Both in filler and canon it's a notion that hagoromo doesn't approve of ninjutsu but only ninshu as je sternly corrects naruto. Meaning Hagoromo after the Kaguya fight only desired Ninshu as the filler sticks to if Hagoromo used ninjutsu you would've pointed that out or maybe not who knows.
Hagoromo literally saud Indra had innovations in other words he was stemming away from ninshu and more towards ninjutsu. Which is why he became a loner, he no longer believed in sharing chakra among others as is ninshu but internalizing and weaponizing it for peace as is ninjutsu. Anyone who can use ninshu can also use ninjutsu I'm not sure about vice-versa.
So there's your answer
1. Yes there is evidence of absence because the manga already concluded. So the burden of proof is on you to prove that Indra had or made Shadow-clones.
2. That's in the real world. But in the Manga it has been made clear time and time again that New Jutsu can be developed like the Edo Tensei, like the Rasengan, and in this case shadow clones. So there is a surplus of evidence supporting the idea that Tobirama actually created the shadow clone Jutsu where as the only thing against it is speculation.
3. Character sketches doesn't mean it's cannon. If kishimoto woke up today and drew Konohamaru killing Kaguya with a rasengan does that mean it's cannon? NO. because it's not apart of the Manga Cannon.
4. They are not.
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Ninshuu = being spiritually aware and capable of the two energies within the body in the form of chakra in order to sychronize mankind
Ninjutsu = Using and developing this chakra to make techniques to kill other people.
The Creation of all things is a Rin'negan technique, not a Ninjutsu and can only be done by having the Rin'negan and access to a surpuls of chakra. Something no one else but Hagoromo would have been capable of. So that excuse doesn't work either.
Yes Indra had inventions but given the ENORMOUS AMOUNT of ninjutsu avaliable in the current day in the NV it could be anything. Saying one of his creations what the Shadow clone jutsu is an assumption and the fact that tobirama said he created it must mean he never saw it before. What did tobirama spend his whole life doing? Fighting Indra's descendants. If Indra know the shadow clone jutsu then he would have passed it on to his children then it wouldn't make any sense of him to say he created it when it would have always been around.