Emulator

This is probably a dual core issue.

I was able to reproduce it on my machine, but only with dual core enabled; for me, however, it dropped to 29.97 FPS, and returned to 60 FPS when the blackness returned. On single core, it maintained 60 FPS the whole time (though the max percentage speed dropped when the whole room was lit, which indicates that the game still is doing extra work of some sort).

Dual core works by emulating the console's CPU on one thread on your machine and the GPU on a second thread. This is generally faster, but it is nondeterministic, meaning weird things can happen if the CPU or GPU thread takes more or less time than usual (see #7143). In particular, this means that updating graphics drivers or having more background programs running can change the behavior - which is likely why this only started happening now. (It also can be affected by Dolphin settings, such as if you increase the internal resolution a lot, then things will obviously take longer to render. But you presumably didn't change that.) Single core, however, is (at least supposed to be) completely deterministic, but it is also slower since since some work for the GPU is done on the CPU thread.

If I recall correctly, the determinism involves telling games that work has finished at about the amount of time it would take on real hardware (though Dolphin's GPU timings are nowhere near perfect), and waiting for that work to finish if your GPU hasn't already, while dual core just lets the game continue to run in that case (only telling it that the work has finished when your GPU says it's finished), though it's been a while since I looked into it. This means that if something starts taking longer, the game will see that the current frame is taking too long to render, and the game will decide to stop skipping frames (lowering the FPS, but emulation continues to run at full speed and the game is still given 60 vertical interrupts per second (VPS) so it still knows how long things should take, which is roughly why the audio still sounds fine). 29.97 FPS would be the game skipping every other frame, while 20 FPS would be the game skipping two frames out of three.

If you want to experiment with the game skipping frames deterministically, you can use single core, and then change the emulated CPU clock override under config -> advanced. Lower values mean the game has less time to do its work each frame, which will lead to it skipping frames (and generally chugging, but audio will still sound fine), while higher values will give it more time within a frame (and if set too high means that Dolphin won't have enough real-world time to emulate things, leading to VPS drops and audio stuttering). For me, increasing the emulated CPU clock override actually avoided the FPS drop with dual core when the darkness effect was removed, since the game thought it had more time and thus didn't need to drop the framerate, but that likely varies. Note that the CPU clock override setting is not accurate to real hardware so it shouldn't be used in speedruns.

I'm not entirely sure why it didn't return to 60 FPS for you when the darkness effect came back (on my machine it does). My best guess is that it's related to CPU/GPU clocking for power usage; at least laptops and phones will change the CPU and GPU clock rates to reflect what is actually needed to reduce power usage, to try and provide the minimum needed. Among other things, this can result in the max speed value being lower than the maximum speed you'd actually get if you held down the fast forward button for a while (as your device would increase its clock rates once it was fully being used). My guess is that on your machine, 30 FPS with dolphin displaying 160% as the max speed is low enough utilization that your machine decides that the current clock rate is fine, meaning that the game doesn't run fast enough that it thinks it can make 60 FPS, leading to a vicious cycle. This is just a guess though, and I have no idea if it would apply to desktop machines. (You can see the CPU clock rate in task manager; I also recommend right-clicking the graph and changing it to logical processors.)

I'm not part of the Super Paper Mario speedrunning community, but I'd recommend discussing it among yourselves whether you should require dual core to be disabled to ensure deterministic behavior or if you want to allow people with weaker machines to also be eligible for submissions (though SPM requiring bounding box already rules out some weaker machines).