I believe I've got it working on citra, and it was actually pretty easy. Any of the many more knowledgeable posters can feel free to correct me if anything I have posted is wrong.
Please forgive the lack of hyperlinks. Gbatemp won't let me post any yet.
To apply the hack itself you will only need a way to extract and rebuild the rom. I used Asia81's HackingToolKit3DS.
Note: the version you want depends on whether your rom is decrypted or encrypted. Decrypted roms need version 9, while encrypted roms need version 11. If you aren't sure, yours is probably decrypted.
To apply any of the patches, such as the unlock all paralogues patch or the early flora patch, you will also need Lunar IPS to apply the patch and BatchLZ77 (there are other programs, but that's the one I used) to decompress and compress the GameData.bin.
Applying the romhack:
1. Create a backup of your rom in case something goes wrong.
2. Download and install the correct version of HackingToolkit3DS. Place your rom in the PackHack folder with the HackingToolkit3DS.exe. Run the HackingToolkit3DS.exe and enter D, to extract the rom. It will then prompt you to enter the name of your rom WITHOUT the file extension. Type that in, then press enter again. The box should then say that it is extracting the rom. This can take a little while, so be patient. When the program is done extracting the rom it will say so, and prompt you to return to it's main screen.
3. After the rom is done extracting, you should have a bunch of files and folders in the PackHack folder that weren't there before. The important one if the ExtractedRomFS folder. Open it, and copy and paste the files from the Gay Hack Luma version appropriate to your rom. The readme in the Luma Version folder will tell you which folder has the files for your rom, so read it. When prompted, copy and replace the files you are putting into the ExtractedRomFS folder.
If all you want is the base hack, then all thats left is to rebuild the rom - skip to step 5.
If you want to apply any of the patches, there are a few more steps - proceed to step 4.
4. To apply the unlock all paralogues patch, first we need to decompress the GameData.bin file. It is found in the ExtractedRomFS\GameData. Download BatchLZ77 and copy your GameData.bin to the BatchLZ77 folder. Run BatchLZ77.exe, click decompress and choose the GameData.bin. When done it will create a larger file named GameData.bin.decompressed.
Next, download and run Lunar IPS. Click Apply IPS Patch, and then choose the ParalogueGameData.ips file downloaded as part of the gay hack folder, in Gay Fates\v0.6.1\All Paralogues Unlocked Patch (this is the patch we are applying). Next Lunar IPS will ask you to choose the file to apply the patch to, which is your decompressed GateData.bin file.
After this is done, run BatchLZ77 again, this time clicking compress, and choose your decompressed GameData.bin file. It will add compressed to the name of the file, and should now be named GameData.bin.decompressed.compressed (assuming you haven't changed the file name yourself). Rename it to GameData.bin and put it back in the ExtractedRomFS\GameData folder, replacing the GameData.bin that is still there.
5. Now we need to rebuild the rom. Run HackingToolKit3DS.exe again, this time entering R to rebuild the rom. It will ask you for the rm name - type it in just as before, press enter, and wait for it to finish rebuilding. The program will say when it is done, and when done will create a new rom file with _Edited added to the name (so if your rom was named Fates, the rebuild rom should be named Fates_Edited). If you applied the gay hack, the new rom file should also be larger than the original.
If you want to apply any other patches such as flora joining early, they are done in much the same way as the paralogues patch. You can apply both IPS patches to your decompressed GameData.bin before recompressing it.
For the Flora joining early patch you will also need to either copy and replace some files in the ExtractedRomFS\GameData folder, or apply further IPS patches if you don't want to overwrite the files being modified (which should only be an issue if you are using other hacks or patches. if all you have applied is the gay hack, there should be no issue copying and replacing, all of which is covered in the readme).
Once you have finished rebuilding your rom, you are done. Run the rebuilt version with citra and consider whether this was worth the trouble or not.
