Well yeah, you uninstalled your menuhacks when you formatted. So what you need to do is go to your themes to let your DS create the file again (delete the old one first) then you need to access HomeBrew again and re-install it.Sorry, not too good with this but !
Yeah, I'm using Reinand with emuNAND.
And no, when I set it up afterwards ( setting the time and date stuff ) the SD card wasn't in it.
Alternatively, you could just go ahead and install A9LH from here https://3ds.guide/.
Then you really don't have to worry too much unless you mess with system apps. You can format all day long and not lose a thing.