If there's no emunand partition on the SD card, it will actually run on the sysNAND, you just won't be able to tell unless you have a different theme or icon arrangement in sysNAND. However, installing a CIA to sysNAND is a risky move - if the install backfires, you run the chance of bricking.
To differentiate emuNAND and sysNAND with a theme or icon placement is a good practice - it'll help you to identify what you're running and prevent accidental upgrading.