Mysql / PHP / json_encode boolean string conversion

Well, you are selecting from the database as string. So that's what gets encoded. Use SQL true/false boolean values, which in PHP become 0/1, and cast them to PHP booleans before JSON encoding them:

$data['id'] = (bool)$data['id']; // 0/1 -> PHP false/true

echo json_encode($data); // {'id':true}