No, it will not work on your updated 9.5 3DS. You have to be on firmwares 4.X-9.2 to use Gateway and all its other features. You will have to get another 3DS on a lower firmware if you want to use it.
EmuNAND is a backup/copy/emulated version of your SysNAND that runs off the SD card. You can use EmuNAND to update to 9.5 while keeping your SysNAND at 4.X-9.2 so you can use the eShop, download updates, games, demos, etc. And yes, you can play 3DS roms on EmuNAND.
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