Emulator

Try starting it up with no Wiimotes set in Dolphin's controller configuration and see if it's still not starting.

Disabling the Wiimote has no effect, the screen still stays black. The other games do not detect the Wiimote anymore, as expected.

I don't know what could be causing your emulated Wiimote to not be detected. Like, if you use the default controls, Emulated Wiimotes should work. IT really doesn't make sense unless you're using the same controller profile between 4.0 and 5.0, and even then that should work...

This disc may not be booting because it does not match any known good dumps of Fatal Frame 4. If it was modified to work in Dolphin under the old regioning system, it may have been modified in a way that would break it in Dolphin 5.0 after we fixed various region bugs. Ensure that your emulated Wiimotes are setup properly in the controller configuration menu. If they're not working in any games, that's likely a minor configuration issue that can be rectified.

I realized that my dump compressed in the wbfs format so I decompressed it to iso and this is the new hash: 2a7d9a23c04bb3b25824052c7e82ecdb. I tried to run the iso with a fresh controller configuration file (I am using the same config profile from dolphin 4.0.2) but the issue is still there.

Please redump the game so we're sure there's not any problems with it. WFBS files won't have the same hash as the original, even if you convert it to ISO.

Try this:
Config -> Wii tab -> System Language: Japanese.

Some japanese games will crash or show a black screen if the language option isn't japanese.

I solved the issue. I redumped the game and now the controller is detected normally. Probably, there was something wrong with my first dump. Thank you for your help.