I think you're confusing A9LH and Luma3DS together.
Luma3DS is just a cfw and using the updater only updates the "arm9loaderhax.bin" file on your SD Card to the latest version.
A9LH is the whole reason why we can do the things we do today on our 3DS' such as no more need of an emuNAND use or 100% Boot Rate to sysNAND and .bin files, etc.
Anyways, whenever it comes to Luma3DS or A9LH, never use anything but the
actual guide itself. Try using
this to update to the SD-less A9LH. Be sure to read all the steps and perform them with caution.