Instant boot > menuhax any day.
I totally get this. But for me - as an almost exclusive Retroarch user - the time saving equation doesn't make sense:
It would probably take me longer than the average 4 hours the process seems to take most. Call it 6 hours, taking toilet breaks / changing of underwear and a mini heart-attack or two into account.
When I switch my N3DS on, menuhax on autoboot gets me into grid launcher and ready to boot an emulator core within 25 seconds, and I can be playing a game within 30 seconds of initial power on.
Assuming that the every super quick A9LH launch saves me, say 20 seconds of time and I can be playing a game within 10 seconds of initial power on, if I play two sessions daily that's 40 seconds saved per day.
By my very rough calculations it'll take me the best part of around 12 months to break even on the time spent installing A9LH. It's just not worth it for me.