If you have avoided all of the above, it might be a good idea to let people know you're still planning a "Final issue" in case they decide to submit whatever they sent you to someone else. Then the following email exchange won't be necessary:
First I want to apologize for the ridiculous amount of time it took for us to get back to you regarding the status of your submission. Due to a number of reasons (Name omitted) Magazine will be shutting down.I want you to know that I fully appreciate the time and effort involved in writing a short story. Thank you for giving us the opportunity to read your work. Unfortunately, we will not be publishing your story in our final issue. Thank you for considering us, and I wish you the best of luck placing your story elsewhere.
Oh, I wasn't even aware you were publishing a final issue. This story was picked up for an anthology months ago.
Can you say "unprofessional?" Sure ya can!