That is, an actual D# played on the actual B string is written as an E on the staff.
It's weird to learn the Kodaly this way, but the piece is hard enough that, at least in my case, I basically have to memorize it to have a fighting chance. I still haven't performed it for a real concert after 20 years of thinking about doing so.
This also creates some ambiguities, since you can play many notes on either the F# string or the D string. But context is enough to tell what Kodaly meant.
Relatedly, the fifth Bach suite is also written for an alternate tuning ("scordatura"), with the same "wrong note" approach to notation (at least in modern editions). The A string is tuned down to a G, giving you beautifully transformed resonances for the key of C minor.
I found that sticking to the edited score's III/IV markings gets you in the right zone–there's enough other things to figure out haha.
Bach's 5th cello suite also uses this technique where the A string is tuned down to a G. (The technical term is "scordatura.")
I wonder if maybe the difference is due to the fact that alternate fingerings are very common for guitar (because of having more strings spaced closer together). So notating pitches assuming a specific fingering doesn't make sense.
Plus I don't think the mapping from the staff to muscle memory for guitar is nearly as strong because we have frets.