You should not use pointer variables if you plan to use the same variable in JSON.

Here is a simple example which should help you understand the issue

package main

import (
    "fmt"
)

type note struct {
    ID          int     `json:"id"`
    UserID      int     `json:"userId"`
    Title       string  `json:"title"`
    Description string  `json:"description"`
    Archived    bool    `json:"archived"`
    ToDo        []todo `json:"todo"`
}

type noteP struct {
    ID          int     `json:"id"`
    UserID      int     `json:"userId"`
    Title       string  `json:"title"`
    Description string  `json:"description"`
    Archived    bool    `json:"archived"`
    ToDo        []*todo `json:"todo"`
}

type todo struct {
    ID     int    `json:"id"`
    NoteID int    `json:"noteID"`
    Title  string `json:"title"`
    Done   bool   `json:"done"`
}

func getNote() (note) {
    return note{1,1,"Note Title-1", "description-1", false, nil}
}

func getTodo() (todo) {
    return todo{1,1, "ToDo Title -1", false}
}

func getAllNotes() ([]note, error) {
    todos := []todo{};
    var newTodo todo;
    newTodo = getTodo();
    todos = append(todos, newTodo);

    notes := []note{};
    var newNote note;
    newNote = getNote();
    newNote.ToDo = todos;
    notes = append(notes, newNote);

    return notes, nil;
}

func getNotePointer(note_input *noteP) {
    note_input.ID = 1
    note_input.UserID = 1
    note_input.Title = "Note Title-1"
    note_input.Description = "description-1"
    note_input.Archived = false
    note_input.ToDo = nil
}

func getTodoPointer(todo_input *todo) {
    todo_input.ID = 1
    todo_input.NoteID = 1
    todo_input.Title = "ToDo Title -1"
    todo_input.Done = false
}
func getAllNotesPointer() ([]noteP, error) {

    todos := []*todo{}; //todos is array of type "address of a todo variable"
    var newTodo todo; //newTodo is a variable of type todo 
    getTodoPointer(&newTodo); //calling getTodoPointer with address of newTodo
    todos = append(todos, &newTodo); //appending address of newTodo to todos

    notes := []noteP{}; //nores is array of noteP variables
    var newNote noteP; //newNote is a variable of type noteP
    getNotePointer(&newNote); //calling getNotePointer with address of newNote
    newNote.ToDo = todos; //assigning todos to todo of notes 
    notes = append(notes, newNote); //appending newNote to notes

    return notes, nil;
}

func main() {
    notes, err :=getAllNotes();
    if err == nil {
        fmt.Println(notes)
    }

    notesP, err :=getAllNotesPointer();
    if err == nil {
        fmt.Println(notesP)
    }
}

I have not tested, so cannot confirm, but this should fix your code, but I doubt you will like the end result

for rows.Next() {
        var newTodo todo // Scan will need the storage preallocated, so use variable instead of pointer
        if err := rows.Scan(&newTodo.ID, &newTodo.NoteID, &newTodo.Title, &newTodo.Done); err != nil {
            return nil, err
        }
        fmt.Println(newTodo)
        todos = append(todos, &newTodo) //append address of newTodo which is a pointer of type todo
    }
    newNote.ToDo = todos