1. Website downtime
Those are ddos attacks. There is basically not much a site can do against stuff like that. If your favorite alternative hoster would get targeted by that, it woud be down a lot too. This happens to much bigger sites too.
2. Adult games being de-indexed from the search engine
That was and is an emergency measure to still have a payment processor. Since the same games are sold on Patreon, this will mostly clear up, even with those payment processors that pressure and blackmail Itch. A more elegant and robust solution would be nice. But that ain't cheap.
If Itch would purge the nsfw content, they would just do that and not give FREE hosting to those developers. You do realize that, do you? Itch does not charge for hosting. Not even if you sell on their platform. It is pay what you want. The industry standard is 30%. Itch suggests 10% and that is not a fixed value. You can change it. And a lot of cheapskates do set this to 0% and complain loudly about services not running and support being slow. That there even is suspport is a small miracle.
Oh, and you might have noticed, that they reindexed games that are not affected by payment processor's threats, because they do not accept payments.
3. Many games suitable of all ages are no longer being indexed
I fail to see that happening. There is 1.2 million games indexed. Not yet indexed things waiting weeks to get indexed is not a new thing and they will get indexed eventually. The way you word that, it implies those things are intentinoally not indexed. That is not true.
And I disagree with your premises with those incentives. Funny that you mentioned GameJolt. They did purge adult games. And they require you to have 1000+ followers on social media to accept you as a developer.
4. Low search traffic volumes for games that do get search indexed
Itch is a file hoster with extra bells and whistles. It is not a game platform for social interaction between users or a platform that will promote the games for you. If you do not promote your own game as a publisher, why even publish. (Oh, one reason might be as a hobby to do game jams. But if you care for selling your game, you need to market the product, not wait for a miracle and be discovered on a game platform that most people do not even know exists.)
You do not need an account to buy a game. You do not need to direct people to Itch to sell your game on Itch. You can embed the sale widget on your own website.
5. Itch.io encouraging publishers on their platform to drive traffic from other sources
That's just Itch telling you, that you need to do your own marketing.
6. Lack of innovation
I wonder what you can innovate about a file hoster where you can buy files. The concept is not exactly volatile.
How do you know that "in-platform search traffic is low"?
It is true that the things are not happening in the public Itch community (these message boards we are using right now.) They happen in some game comment sections and mostly not at all, because, as I said, you buy or download games here. You do not even need an account to buy.
The first time I encountered Itch, I did not know what it was, and the site was over a decade old. And I did not encounter the page as such, but only the game that linked me to it. I knew some famous games that emerged from Itch, but not that they did emerge from Itch. It still is an obscure indie site. It is for self publishing game developers and hobby game creators. People inbetween hobby and profession. And yet another place to publish your game, with certain incentives and some quirks. It is cheap, even if you pay more than the recommended share. And you have much control over what you do.
Itch is abused right and left by criminals and on top threatened by bigots and ill treated by cheapskates. All this is concerning, since Itch is a place for indie game development. And there are not many such places. I do not really know any other. But I did not know Itch before, so that's not saying much.
Anyway, the incentive to use Itch as a developer is for self publishing. You can do that with a bare bone file hoster too and Itch even supports this by allowing links to other file hosters. You can also link to other stores. Are there any Steam pages that have links to Itch, Patreon or GoG and other's? It might seem foolish by Itch, but so is pay what you want. Itch is not only a place for indie games, it is itself rather indie. For good and for worse.