I have two kinds of references in NTN. One is flat out obvious, and one is more subtle. The first is referencing something that the reader can understand flat out - like the first reference being to Alice in Wonderland and following the rabbit down the hole. The second style I utilize is usually through dialogue but can also be through setting - and it's taking a portion of a line of a song, or paraphrasing someone, from a game, movie, anime, ect - but these I never reveal to the reader.
I can see them myself very easily, but I think if I pointed them out to the reader it'd lose a sense of wonder. Some of them flow so well with the existing story that I don't think many realize I've done it. I've never had a reader be like "omg i see you quoted this line from xyz!" before, so they must be pretty well hidden. It's one of those things that if someone sees them, I wouldn't deny it. But if someone sees a line of text that isn't a reference and says it is... bleg, that's not fun.
As for cameo characters, 99% of the characters in NTN or other stories are made for the story and meant to be there. They aren't cameos of other people's characters or anything. A few cases stick out that they are cameos - such as Isaac is re-purposed character and design from a story that never got off the ground, and Isaac is the same - their involvement in NTN is minimal, and yet impactful. Another small "cameo" of sorts is way later on where I reference the King has 13 knights - it's a callback to an earlier story I've written where the main character is protected by 13 knights of eld. Less so with Isaac, but I've been very clear with Akiio that it's the same Akiio as the one from the failed story- and I even reference that he failed in his mission to protect someone (a person he came to love).
But all of these little cameos I don't think readers will notice if they haven't been on my writing journey. It's one of those things that if they dig around through my dA and writing material they'll be able to see it (though the 13 knights one currently isn't online in its entirety so that one might be super hard to spot lol).