It sounds like it's not unheard of for them to make game-time changes to their 9-course menu...for example, when one of the courses was planned to be chicken liver, a few folks got pork belly in its place (yum! lucky). I would imagine that the reverse could just as easily happen.
That said, the current 9-course menu looks pretty tame, except for the natto and the pickled beef tongue. Personally, I would recommend just going with it, and taking a nibble of anything you find questionable. If you don't like it, you can always eat around the offending ingredient or push the whole plate aside.
The worst-case scenario is that you'll eat 7-8 of the 10 courses you'll be served (they snuck a bonus dish into the middle of our 9-course, the dreamy, highly-acclaimed quail egg ravioli...I could've eaten a whole bowl of those things), and you'll leave there plenty full.
The best-case scenario is that, since you won't recognize half of the stuff on the plate anyway, you'll get to taste things without any preconceived notions or established prejudices, which isn't something people often get an opportunity to do...usually, you see caviar, you know you don't like caviar, so you don't eat the caviar. But here, you and your husband could take a nibble of the mysterious-looking, green-hued little pile on the corner of your plate, and find it to be delicious...whaddaya know, you just ate & loved caviar!

But if you aren't willing to nibble at the often-unidentifiable morsels on your plate for fear of accidentally eating something gnarly, or if you think getting a taste of something you really don't like might put a damper on your mood, then the 3-course might be a better fit (plus the options look pretty tasty, especially the Chimay-based beer-cheese soup).
If your reservation is at 9pm, you won't get out of there before 11 (midnight is more likely). So if that's too late for you, then maybe the 3-course would be the way to go.
Whichever you choose, it'll be a very memorable experience! I hope you both have a blast!