Shaders can cause problems (I am not saying that they will cause problems, I am saying that there are some cases where they cause problems), it is recommended to test without a shader to ensure that this is not the case. Overlays can also create problems when configured incorrectly or at a higher than ideal resolution.
I don't know this case, but, for example, retroflag's cases have a script for safe shutdown (which also turns off the fan), maybe this nes3pi case has some similar option, but I can't guarantee it.
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Perhaps this will interest you: