Every valid string can be a valid key in JSON. So parentheses in key names are possible.

It is up to the application to interpret the content of the parentheses.

You should use a callback parameter in the url you provided for accessing the data. Because the data interchange format is jsonp. Those parenthesis are probably added because the callback is being evaluated as an empty string.

See the example below with the url you provided.

https://getbible.net/json?passage=1samuel3:16&v=cus&callback=foo //foo is the callback name

It returns the data with the callback name foo.

foo({"book":[{"book_ref":"1 S","book_name":"1 Samuel","book_nr":"9","chapter_nr":"3","chapter":{"16":{"verse_nr":"16","verse":"\u4ee5 \u5229 \u547c \u5524 \u6492 \u6bcd \u8033 \u8bf4 \uff1a \u6211 \u513f \u6492 \u6bcd \u8033 \u554a \uff01 \u6492 \u6bcd \u8033 \u56de \u7b54 \u8bf4 \uff1a \u6211 \u5728 \u8fd9 \u91cc \uff01\r\n"}}}],"direction":"LTR","type":"verse","version":"cus"});

See the example below which shows how to access the data.

var url="https://getbible.net/json?passage=1samuel3:16&v=cus&";
var callbackname = "callback";
$.getJSON(url+'callback=' + callbackname, function(json){
    //loop through data
    $.each(json.book,function(i,dat){
        document.write(dat.book_ref); //print the book reference "1 S"
    });

});

You can convert string contents into an array. But you habe to iterate over all answers for this purpose.

Creating an array with an if-condition

<?php
$json = '{
  "question1": "answera",
  "question2": [
       "answerb",
       "answerc"
  ]
}';

// second parameter for array result
$array = json_decode($json, true);

foreach ($array as $question => $answer) {
    if (is_string($answer) === true) {
        $array[$question] = [ $answer ];
    }
}

This one results into ...

array(2) {
  'question1' =>
  array(1) {
    [0] =>
    string(7) "answera"
  }
  'question2' =>
  array(2) {
    [0] =>
    string(7) "answerb"
    [1] =>
    string(7) "answerc"
  }
}

For any further JSON processing you can convert the PHP array back into JSON.

$json = json_encode($array);

Results into ...

string(109) "{
    "question1": [
        "answera"
    ],
    "question2": [
        "answerb",
        "answerc"
    ]
}"

Casting with (array)

Another solution taken from the comments was mentioned by @RickN. Casting with (array) avoids the if condition and could possibly be faster, if that matters for your application.

foreach ($array as $question => $answer) {
    $array[$question] = (array) $answer;
}