It's a serious issue, but to some extent this is true of any service that depends on someone else's computers.
However, you can mitigate this by trying to find out more about the person running the instance, what their track record is etc.
One useful link:
fediverse.network/yourinstancehere
This gives you an idea of recent uptime, what version the software is etc.
Also, on Mastodon, the joinmastodon.org site only lists instances that have proper backup plans in place.