The only issue you may run into is if you left your 3DS on with the wifi on, on your regular system NAND. If you did that, your console may have already downloaded but not installed the update, and when you try to update your emuNAND, it will constantly fail. The only solution I found was to format your system completely and reinstall Gateway, back up your NAND again, then format the emuNAND, then update the emuNAND.
This update is very minor. It only updates the eShop.
Whenever you see only the final numbers in the firmware version changing, it's just a small update to the eShop and won't affect anything else. You're totally safe to update your emuNAND.
Also, do not listen to anyone except for people who actually own a Gateway card. Don't buy into the hype. Run 2.0b2 if you want to. You have less than a 7% chance of bricking. I've booted into Gateway Mode well over 200 times from having my 3DS powered off completely, and have experienced zero issues.