Yes, but it's possible to boot without SD if you upgrade a9lh to the experimental branch made by aurora wright.
No need to worry about it, arm9loaderhax works before the firmware boots, so it doesn't matter what version the firmware is on. You can use other entrypoints like the homebrew launcher CIA to boot the HBL. You can use decrypt9 to downgrade if necessary
Yes, it is impossible for nintendo to patch this
No, it's not better because of how a9lh works. However, if there are reasons you need an emunand (like testing something or region swapping), you can still use one. Some drawbacks include less SD card space, potentially slightly longer boot times, and you can't use your 3DS without an SD card in.