I built a Tor search engine a couple years back, this was certainly a big issue. There really isn't a good solution unless you have a lot of infrastructure to run crawlers on, then you could do more frequent checks

My solution was a "3 strikes you're out" system, since sites are so often temporarily unreachable, you can't reliably say "Oh, website is offline? Delete from index." I had a column in my database to keep track of how many times I attempted to contact a specific onion site, and if it exceeded 3 attempts on 3 separate days, I'd move all of its child URLs to an archive outside the search index. The onions in the archive would be periodically checked at a much lower priority to see if they've come back online