Absolutely. We've already set outselves up for eventual failure.
I was speaking to a friend registered with the tech.lgbt mastodon instance, and all I could think was "that sure makes that population vulnerable". There's so many instances that were paid as a one year server subscription by a hobbiest who might lose interest, and poof - those instances will be gone without warning.
Search will get better across instances over time. Instead of thematic instances, I'd really like to see focus on instance governance:
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Which are run by corporations, non-profits, academic institutions, or cooperatives who have an accountable board incentivized to maintain their instance?
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What are their sunsetting plans? Do they have policies in place to warn users if they become unsustainable?
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What are their funding models, and how well equipped are their technical staff?
As a librarian, this question tickles me.