If he has a variety of art that is produced I wouldn't over think it. There are thousands of reasons that you can come up with on why he decided to produce some dark art. Many pre-schools do the scratch paint with children, where they color underneath and scratch of the top black layer to show color.
I think you are doing a good job praising his art effort. There is nothing asking him to tell you about his artwork.
If your worry continues. Do you some art projects with him at home. Watch and talk to him during the art project to maybe get insight into his thoughts and process. It is awesome that you are this aware of what your child is doing. I really wouldn't over think this one, however if any concerns persist, talk to the pre-school again.
I hope that I have put your mind at ease. However if there is anything else, don't hesitate to let me know.
I see you are in the chat now. Question? Is your child producing other types of artwork? ie. is he adding color on other pieces of art?