Does it happen consistently for you? I tried to reproduce it on my 3DS but I wasn't able to.
I tried it again today. After opening the app (without any game open, just after the boot of emunand) the bug happened again. The first time the power button worked just as normal but after opening the app the second time the button does not react anymore. I'm testing it a bit atm and i am able to go to sysnand through the system settings reset in emunand, the power button works again also when entering emunand again. This time after opening the app once, the power button got locked again. Maybe it bugs because there's no game open? i'll play with it for a bit and edit this post.
Edit:
Ok so i tried it with some games. The power button got locked and i started supersmash. The game exited as intended and the powerbutton got unlocked again. So the app is working great, as there is no reason to open the app without playing a game anyway. But still it's nice to know such a bug is present (or unintended system change or whatever)
Anyway I love it, thank you!