If I recall correctly, RxTools emuNAND cannot be updated to the latest version because it uses some obsolete files. Luma3DS uses more current files, so it can be updated fully. RxTools also interferes with the 3D effect, causing noticeable ghosting effects which can accelerate how quickly a player's eyes tire from using said 3D effect. This issue is not present with Luma3DS either. The main benefit to RxTools was the "Tools" part of the name, in how it could do a variety of additional things to your 3DS. The thing is, these tools are obsolete, and their standalone counterparts are more stable and currently updated.
Long story short, eventually you'll want to play a game that will require a firmware update that RxTools simply cannot handle. It's much easier to swap to the more up-to-date CFW that will be able to deal with it now, rather than after you attempt to do the update and mess up your EmuNAND.
Now, I have my own two cents that I'd like to put into the conversation. Yes, I'm aware of the benefits of using Luma3DS over RxTools, and I recently swapped over. However, I'm still using MenuHax for my own system. Why? Because the guide is designed from a stock system to the final result. I currently have an EmuNAND that has a number of games, homebrew, and emulators installed. I tend to play longer games such as RPGs, and so losing my EmuNAND with all of my save files is a bit of a concern for me. Furthermore, while I have a back-up NAND file already from when I set up my EmuNAND the first time, I'm not entirely certain where in the guide I'm meant to continue. I believe that I'm at the point where the only thing left to do is to run the SafeA9LHInstaller program. However, I still have a measure of uncertainty about that, and given the possible risk of bricking my system if I'm wrong, I decided that the safest approach is to just stick with MenuHax. I don't usually let the batteries run dead, and tend to recharge them when the light starts blinking, so the longer boot time is rarely a concern for me. On top of that, while I admit that EmuNAND is potential wasted space, I tend to only play a couple games at a time, and delete games that I've finished (while keeping the save data in case I want to play it again and re-install it), so my SD card is usually large enough for my needs.
Furthermore, if you think back to when MenuHax was the most recent entry-point, a common trick was to use two different colors to help differentiate between the two NANDs. Personally, I'm rather fond of the black color scheme, so I have SysNAND set to the red theme, and EmuNAND set as the black theme. MenuHax is also set to auto-boot into EmuNAND, so the risk of updating SysNAND is miniscule at most, and I can easily see if I've somehow booted into SysNAND, although that's never happened once I set up the auto-boot feature.
As much as everybody keeps saying that MenuHax is obsolete, I don't see a massive need to switch to A9LH at the moment. Yes, it's no longer updated, but it does what it needs to well enough for people like me. Unless I'm mistaken and there's another benefit to switching? I can understand urging people to swap from RxTools because it can lead to a major problem if not taken care of ahead of time. I don't see such an issue to using MenuHax once it's fully set up, so why does it seem almost hostile towards people who still choose to use it?
