I have a 11.0.0-33U SysNAND and a 11.0.0-33E EmuNAND that way I can play European titles on the EmuNAND without "compromises" like the manual not working or being asked for a PIN.
For some the biggest advantage might be that you can double the number of installed eShop titles (keep in mind to install TWL and AGB titles on your SysNAND, but any 3DS titles that are not US-exclusive can go to the EmuNAND). And vice-versa for European (n)3DSes of course.
I still have my 9.2.0-20U pre-A9LH SysNAND backed up of course so it's easy to roll things back.
Can you explain the details regarding the doubling of eShop titles if you have emunand? (especially explain niche things like the TWL and AGB thing that you mentioned since I don't know what they are.) The doubling of eShop titles is something that I didn't know about and it would indeed be a worthy reason to use emunand.
Also, an additional advantage to using emunand is to be able to use public WIFI on the N3DS. Normally, to use public WIFi, you open your internet browser and are directed to a login portal and must accept the terms and agreements before you are allowed to use that location's free public WIFI. With the N3DS, if your firmware version is above a certain number: if you try to connect to a wireless network at let's say a Starbucks, McDonald's, or Shopping Mall; then the console boots you out of the internet browser with the message: "The Internet browser cannot be used at this time. Please check your network environment or try again later."
The reason why this occurs is that if your console senses that you are not connected to a wireless network for 10 seconds; you are booted out, which means that you don't even have the chance to be redirected to that login portal.
This creates a paradox: In order to connect to a wireless network (Public WIFI), you need to already be connected to a wireless network. Essentially what this ultimately means is that you are locked out of using Public WIFI using just the console and unless you use some convoluted method to access said wireless network by coupling the usage of your console with something like a laptop or Smart phone, you're basically fucked. Blame Nintendo for including this worthless Internet Browser patch that shuts you out of your attempts to connect to Public WIFI (wireless Network).
NOW LET'S GET TO THE GOOD PART. HOW DO I BYPASS THIS WITH EMUNAND?
The answer is simple. If you set up your EmuNAND so that it is on the latest version and your SysNAND is on version 9.2.0-20, what you do is use your internet browser on the NAND that has 9.2.0-20. The internet browser that is on this system version, pre-dates the N3DS firmware patch that boots you out of your internet browser after 10 seconds if you are not connected to a wireless network. Since 9.2.0-20 pre-dates this patch, you are able to successfully connect to the Public WIFi (Wireless Network) without a hitch. Once that's done, switch to EmuNAND which is on the latest version and enter the internet browser again. This time, because you connected your console to the local wireless network on your SysNAND; you will not get booted out, and will have the opportunity to access that login portal that was always out of your reach.
Once you accept the terms and agreements of the login portal on your EmuNAND, then VOILA. YOU NOW HAVE ACCESS TO PUBLIC WIFI ON YOUR N3DS ON THE LATEST VERSION (albeit on EmuNAND but who cares? I get to trade Pokemon online again!)
P.S. Remember to Unlink your NANDs. Failure to do so will result in having that annoying gift wrap bug forcing you to unwrap all your CIA installed games every time you enter EmuNAND.