There are no real consequences (as in everything you'd expect works just fine), but there are some things to keep in mind.
Since the system is region-locked, to get started with Gateway you have to have a Japanese copy of Cubic Ninja or OoT. It might be preferable to just get a sky3ds as your baseline exploit, because it's only a little more, can function as any region card if you decide to region swap your system later, and if you botch up Gateway at least you have a functioning flash card to use on any firmware. At the very least I'd highly recommend Cubic Ninja over OoT now, since CN is useful for more than just the initial Gateway exploit.
Japanese 3DS systems do not have English as an option, so you will need to learn to navigate the system settings. This isn't super hard when you get used to where things are, and there are cell phone apps that can straight up take a picture of Japanese and translate it for you if you're afraid of doing something you shouldn't. More importantly, there are 2 unexpected side effects of this language issue, but they can be worked around. The first is that games that have a EULA for online will throw an error when they try to display on your system. The workaround for this is to find a file called config.csu, rename it to config.3ds and run it. Change your EULA setting to ff.ff. The other issue is that games with multiple languages may or may not use the system's language to set their own, and may or may not have in-game settings to change it. 3ds files tend to go by the region of the rom probably due to the spoofing Gateway does to run it in the first place, while cia files tend to go by region of the system, but even this has exceptions. A workaround for cias is to hover over the cia you want to region-force, open the multi-rom menu, go to a 3ds file of the region you want to force, then select it and immediately launch the cia before Gateway finishes loading the 3ds file to the system menu.
There are no issues with online play I can think of. Pretty much everything works on the region of the rom rather than the region of the system, but because you only have access to the Japanese e-shop this means you'll have to obtain and install all of your updates on your own as cia. You'll also need a Japanese NNID to download demos on the eshop. I'm not sure how buying things would go, but I'd guess your only option to legit buy stuff would be to buy pre-paid eshop cards.
There are methods to region swap, but you'd need a donor file from a console of the region you want to swap to. The process is probably not as simple as you'd hope.
