How can I work with SQL NULL values and JSON in a good way?

Types like sql.NullInt64 do not implement any special handling for JSON marshaling or unmarshaling, so the default rules apply. Since the type is a struct, it gets marshalled as an object with its fields as attributes.

One way to work around this is to create your own type that implements the json.Marshaller / json.Unmarshaler interfaces. By embedding the sql.NullInt64 type, we get the SQL methods for free. Something like this:

type JsonNullInt64 struct {
    sql.NullInt64
}

func (v JsonNullInt64) MarshalJSON() ([]byte, error) {
    if v.Valid {
        return json.Marshal(v.Int64)
    } else {
        return json.Marshal(nil)
    }
}

func (v *JsonNullInt64) UnmarshalJSON(data []byte) error {
    // Unmarshalling into a pointer will let us detect null
    var x *int64
    if err := json.Unmarshal(data, &x); err != nil {
        return err
    }
    if x != nil {
        v.Valid = true
        v.Int64 = *x
    } else {
        v.Valid = false
    }
    return nil
}

If you use this type in place of sql.NullInt64, it should be encoded as you expect.

You can test this example here: http://play.golang.org/p/zFESxLcd-c

If you use the null.v3 package, you won't need to implement any of the marshal or unmarshal methods. It's a superset of the sql.Null structs and is probably what you want.

package main

import "gopkg.in/guregu/null.v3"

type Person struct {
    Name     string      `json:"id"`
    Age      int         `json:"age"`
    NickName null.String `json:"nickname"` // Optional
}

If you'd like to see a full Golang webserver that uses sqlite, nulls, and json you can consult this gist.