What should you ask an applicant's reference?
This may well depend on the country. In the US, being the litigious society that it is, there have been some people going after (legally and non-legally) people who give negative references. The candidate can have a stronger case if you are contacting someone they didn't approve. Now, there is freedom of speech and many, many other issues but simply put, some people in the US are scared to give candid assessments unless the assessment is positive.

So, I would tend to take the response you received as an implied negative but I would also have to keep an open mind that the referee simply did not want to answer and it might not reflect at all on the candidate.

As for the questions you ask, they seem quite standard and I don't believe anyone would be taken by surprise by them. However, they might not answer out of fear.

On a side note, when it comes to reference checking, you need to be sure you are getting are response from the proper person. Emails get hacked, fake accounts get created. I personally prefer doing my reference checking over the phone. This may also come across as a casual conversation without written evidence, making the referee more comfortable in being candid.