Question in the title.
Has an entire thread ever been deleted for any other reason then that it was started by a sock? I’ll bet that’s the case 99.9% of the time.
Well, there are the ones from spammers.
Anyway, wouldn’t putting in a note along the lines of “The thread titled ‘Could we solve the crime, overpopulation and hunger problems by killing all the niggers, making them into sausage, and giving poor white people free nigger sausage’, started by Guest ‘Fuck you Tubadiva I’m back’ has been deleted for being trolling and sockpuppetry” kind of defeat the purpose of the deletion?
Plus, if the thread is gone (cue BB King), where would you put the notice?
Did they delete the thread where the woman asked if her boyfriend’s relationship with his niece was incestuous? I posted in it and then searched for all my own posts, and it didn’t come up. I do remember someone suggesting it was a gawker advice column duplicate.
That’s the one that prompted this OP, but I wanted to avoid referring to it specifically, not knowing what the reason was.
In ATMB, of course.
You’ve put your finger on the problem: I *do * know what the reason was, and so want to avoid referring to it specifically. That leaves us with something like, “We may have wished away a thread today, and even if we did, we wouldn’t tell you why.” 
I would think everyone knew the rule by now. Threads, posts, etc. disappear when they are the work of undesirables, specifically sock puppets. The Powers that Be remove their handiwork so that they don’t get any gratification from their limited period of presence. If there was an announcement about it in ATMB, that alone would act as attention and gratification.
So if it’s been disappeared, just assume it was the work of a sock and restart it if you feel it had merit of its own. If you have questions about a specific thread, e-mail a moderator.