As of early November 2025, PSE has gained the ability to put spoilers in comments; see Spoiler tags in comments for the announcement.
Accordingly, if you were contemplating using ROT13 to obfuscate something in a comment, please now use the spoiler-in-comment syntax instead.
I don't think it's worth the trouble of going through old ROT13-ed comments and converting them to the new syntax, though doing so in any particular instance would clearly be an improvement and I think present or future Puzzling mods with nothing better to do should feel free to do it :-).
I make no guarantees of whether the mods will bother to fix up new rot13-obfuscated comments if they are flagged; my guess is that generally we won't.
As for good commenting practice now that we have the ability to put spoilers in comments: (1) do use the spoiler feature for anything spoilery in comments on a question because casual readers who would prefer not to be spoiled may well see those; (2) use your judgement about comments on an answer because most people reading comments under an answer will also have read the answer itself. You might, e.g., be more inclined to spoilerize such comments when they introduce new potentially-spoiling information.
(I think my own practice will be to apply spoiler markup to anything spoilery in any comment I write, for what it's worth.)
[I have written the same thing as an answer to https://puzzling.meta.stackexchange.com/questions/4649/how-do-we-deal-with-coded-comments/ .]