I do not think marriage has to ascribe to a set of rules conveniently laid out by religion or cultural mores. To many people here honesty and openness is a really important value, but interestingly to Japanese it is actually not the most important thing for a lot of people.
To this end, OP needs to understand if it is or isn't the most important thing to his partner. I get the feeling OP doesn't necessarily really know what his partner is feeling/thinking and is just assuming or trying to read the room.
My advice to OP is:
Don't make a brash decision one way or another; wait 6-12 months and see how you feel. But, between now and then, have the talk with her about all this. Understand why (or if) she doesn't actually like sex - has she had a trauma like a rape she has never told you about? Was she a provider at one time? Are you selfish in bed? Does it hurt her? Are you just not that compatible/good in bed? Are you only interested in the physical part and not giving her the emotional part she needs outside the bedroom? Also find out what her expectations are now and in the future (but probably take what's said about the future with a grain of salt if it sounds great), and what she would think about your happiness and getting your needs met elsewhere if she's not that interested. I was with someone once who "wasn't that interested" yet at the same time, wouldn't let me do anything outside either. What a crock of crap that was, clearly my happiness didn't matter. Yes, she was Japanese. And yes, my resentment for her bred, and bred, and bred, and bred trying to figure out what was so damn undesirable about myself.
And I can speak from experience on the future of your sex life and back up the others - it WILL decline from where it is today, with a VERY high chance of it declining to absolutely zero - and very likely with no words ever being spoken about it and it becoming a completely taboo subject to the point where if the two of you are watching a movie and a sex scene comes on, it gets really awkward.
I would also understand the implications of divorce and how easy or difficult it may be. Sure, you can do mutual consent divorce in Japan and just go fill out a form at city hall and it's basically a done deal if you both agree on how to split stuff up, etc., but guess what? Some countries won't recognize that and will require a signed decree from a family court judge. So you might be able to get divorced in Japan, but NOT be able to get remarried outside Japan without a decree signed by a judge; or maybe you could due to lack of international coordination on that kind of stuff, but you might find that in order to be truly out clean in a way that is recognized everywhere, you need a signed decree. It's kind of a gray area in that at least in the US, the US requires no proof of a Japanese marriage at all, yet in some states, if you want to get divorced, suddenly they care about the manner in which it was done and a mutual consent isn't good enough when you never even had to prove you got married in the first place and they just accepted you at your word when electing to file taxes as a joint married couple? Makes no sense. Rambling, but the point here is - understand
everything to the best of your ability, both personally and legally.
Good luck OP, and let us know what happens - one of the biggest challenges will be having any talk with her at all because you are definitely kind of western culture gaijin smashing her by trying to do that, in a country where even mothers and daughters don't always talk directly with one another and do the read the room bullshit around each other on stuff. Just having a successful, fully open and transparent conversation may be more difficult than you think.