Normal- nothing to worry about- It makes sense that she doesn't want people messing with her in the dark. Think about if you shut the lights off in your toddler's room and then made weird noises after they thought you had left lol...or pulled on their cover ha!
Mine (cockatoo) doesn't do this until she is actually falling asleep or if she is woken from a sleep( **usually** at least 1 hour after she is covered). When I first got her, she did it very easily (right after going to bed)...Now it usually has to have been quiet for quite a while before she will get that freaked out.
I know this because sometimes I put her to bed and then I have to move something really near her cage. In these cases, I often hear hissing (or if I brush up against the cover etc etc).
When I first got her, I didn't know how easily cockatoos hissed when scared, and the first night she was home (being a very nervous mother), I walked near her cage to make sure there wasn't a draft by the window. I also put a towel down at the base of the window and adjusted her cage cover slightly. Then, I heard that CRAZY sound and I was so worried about her lol! I knew why she was hissing, but couldn't help but check on her with a flashlight to make sure she hadn't had a heart-attack in there. Needless to say, she was not a fan of my thoroughness.