My sysnand is on version 7.2.0-4U and im currently using emunand 11.2.0-35 because thats as far as gateway goes for the moment.
can you still access the system menu normally?
I feel like a small explanation is required here.
Basically, what Boot9Strap is, is an flaw in the way the bootrom checks the firmwares you give it. When you press the power button, the bootrom is initialized, which is essentially the initial program loader.
The flaw that was found is that there is a special signature with which you sign the firmware you want to load, and the bootrom will always read the firmware as valid,
even if that firmware you are trying to load is not made by nintendo.
So what is done, is we gain access to write to the NAND some files through an ARM9 exploit (The 3DS has two processors, the ARM11 and the ARM9, the ARM9 acts as a security processor), and we write some special files to our NAND (Since only the ARM9 has access to writing and reading to the NAND). These special files tell the 3DS to load .firm files (Our Custom firmware) from the SD card, and then we sign the entire NAND image with with that special signature which is always read as valid, we call this
sighax. Here's some technical info:
So, every time you open up the 3DS by pressing the power button, there is nothing of the sort of emuNAND, or anything like that. You press the power button, and instantly you load the custom firmware. You don't have to go to the web browser, or to the system settings to go to the DS profile option, or anything of the sort.
Therefore, yes, you can access the system menu normally. In fact, it is technically the only menu you can see, apart from GodMode9 (A file manager built from the ground up, for the 3DS, that is open source) which you can access by holding START when your 3DS boots up, or Luma's configuration menu (Luma is the CFW you will probably install, and this is what patches signature checking and allows us to run our own code, in the form of homebrew, or dumped 3DS games that have been converted to .CIA format) which you can access by holding SELECT when the 3DS boots up.