Well this is way OT. Anyway:
I am not rich enough to backup every single thing I collected. I have more than 5TB for my collections. Even if I have backups, it is no joke restoring 5TB worth of data.
Why risk the HDD when I don't have to.
Running with or without SD doesn't make much a different except it is a bit slower and bootmii will look for a bootmii folder in SD and auto-run a certain files from it at boot. If that folder contain corrupted or bad files, that may cause problem.
And see what the Pro/dev recommends:
https://gbatemp.net/threads/usb-loader-gx.149922/page-1083#post-6013233
But if you are running fine now, then "don't fix it if it ain't break"