w00t another 3D Godot dev!
I also ran into audio issues with my HTML5 exports and came up with a workaround to fix it. It was kinda complicated so I posted a description of how I did it: https://3p0ch.newgrounds.com/news/post/1148893
I'm not 100% sure this will also fix it for you but I think it's more likely than not.
Edit: Finished the game. The 2D-in-3D graphics were appealing and had a lot of nice touches, the creepiness of the things in the containment rooms helps make the game memorable. The design of having the player go into a J shaped area when they kill the power and have the monster where it is pretty much guarantees that the player will die the first time through and have to start from the beginning, and if they don't notice that the monster moves through walls right away then they'll probably die at least once more, each time having to start from the beginning. It's a short game so it's not horrible to have to repeat the path to the power room each time, but it's kinda monotonous to have to do each time before the real action starts. After figuring out how to really play the game, it's entertaining enough to make up for it. Looking forward to seeing what you do in the future.