The JSON is data only, and if you include a comment, then it will be data too.
You could have a designated data element called "_comment" (or something) that should be ignored by apps that use the JSON data.
You would probably be better having the comment in the processes that generates/receives the JSON, as they are supposed to know what the JSON data will be in advance, or at least the structure of it.
But if you decided to:
{
"_comment": "comment text goes here...",
"glossary": {
"title": "example glossary",
"GlossDiv": {
"title": "S",
"GlossList": {
"GlossEntry": {
"ID": "SGML",
"SortAs": "SGML",
"GlossTerm": "Standard Generalized Markup Language",
"Acronym": "SGML",
"Abbrev": "ISO 8879:1986",
"GlossDef": {
"para": "A meta-markup language, used to create markup languages such as DocBook.",
"GlossSeeAlso": ["GML", "XML"]
},
"GlossSee": "markup"
}
}
}
}
}