Last time I looked into Mastodon (a couple years ago), I found a small, specific community that piqued my interest. Months later, the owner of the instance lost interest and closed it. In the end I never registered, but, what would have happened if I did and started to use it in my day to day? Would I wake up one day to find out that I no longer have a Mastodon account?

I feel the response might be something akin to "what would happen if you have a fastmail account and then fastmail closes?". If that's the case, I see absolutely no reason to choose a small instance, just for the sake of reliability and trust in its continued operation.