When you download an app from the official App Store, your iPhone downloads an IPA file silently in the background and installs it. However, when you want an app that Apple has banned (like a 3DS emulator), you must find the IPA file online and "side-load" it onto your device using a third-party installer.
Not all iPhones are created equal for 3DS emulation. Ios 3ds Emulator Ipa