Solution (which everyone else does, and OP has now implemented): don't use your ISP's recursive resolver! Run your own instance of bind9 or whatever, with the cache disabled. Or it seems like `dig +trace` would probably work, too.
"Cached resources remain visible for their whole TTL, even if the original becomes unreachable or changes" seems like one of the very first principles someone should learn when deciding to go into business selling an uptime monitoring service.
It's not a "ghost domain," it's a Time-To-Live field!
But I think there is a real issue if caching recursive resolvers don't revalidate delegations. If .com tells you the example.com nameserver is ns1.example.com with some TTL, and ns1.example.com tells you its the nameserver for example.com every time you ask for www.example.com, you should still check in with the .com nameservers ever TTL to validate.
I'm not surprised the default behavior doesn't do that, because when I migrated a high profile domain to new nameservers, we still saw requests to the old servers for more than a month... but it's still ugh, recursive DNS should do better!
My understanding of their implementation is that it does caching on a per-worker basis with lower TTLs, so it balances caching with accuracy, but doesn't "fix" visibility to the problem either. However, it narrows the window such that their method of monitoring will very likely expose a pulled domain sooner.
https://static.sched.com/hosted_files/icann83/5b/Rafaelle%20...
Quad9 (9.9.9.9) consumes this feed from U Twente of "just deleted" names, as most of them are malicious, and blocking them even if they are NOT malicious causes zero harm. Currently, this is only names that are very short-lived, so may not catch the longer intervals where names are deleted and become ghosts.
Another model using something similar would be to specifically clear those "just-deleted" name cached entries out of the recursive resolver, but that is expensive. Also, with blocking instead of removal it is possible to get high-level metrics on how often those are being abused where NXDOMAIN tracking is not measured in the same dimensions.
(disclaimer: I work for Quad9)