Unless you routinely sit (and rise!) in seiza while wearing a constricting skirt, I'd advise wearing under garments with a ryokan yukata. Some ryokans serve dinner in banquet halls where you sit on tatami mats. Western female travelers beware the seiza and take your time getting in and more importantly out.

In my experience, the procedure usually goes this way:
1. Try to kneel while edging up to a tray holding dishes that are quite expensive, some lit on fire, and in a nation that does not acknowledge the three second rule.
2. Give up trying to kneel while tottering and just slowly edge into a slightly gracious cross legged bend and rearrange legs properly. Try not to flash people.
3. Maintain for a while until legs fall numb or pain sets in. Try not to be distracted from food by pain in legs slowly falling asleep.
4. Attempt not to flash anyone or spill dishes while I scoot very numb legs towards the front. Unladylike but I'm probably not the first to cave in. This is usually difficult as once you move, you regain sensation in the limbs.
5. Arrange legs sticking straight out in front. Come to realize this will also hurt in a while. Wonder how many more courses of kaiseki there are.
6. Surreptitiously re-tuck yukata on top as I've probably tied the belt incorrectly. Again.
7. Eating finally over, attempt to rise and flee the upcoming karaoke as fast as possible. This may take longer if you're not willing to be the first one to leave. Ignore any popping sounds from joints or limping, especially if demonstrated by others.

If you are unlucky, you will meet someone who isn't wearing underwear and you'll notice it while dining. And it will be the man who can't sit cross legged, legs forward, or anything remotely decorous for sitting on a floor. And his top will gape. Then if you're seriously unlucky, he'll also have his yukata on the wrong way, have worn the toilet slippers to the dining hall, and is tone deaf. You do not want to be "that person".

Granted most individual travelers probably don't have a group kaiseki experience followed by karaoke... But just in case...

All this aside, the food is totally worth it. I enjoy the experience even with numb legs. You can always check pictures of the dining hall to see if there will be a small pit for your legs or if chairs are used. It helps to have the chair backs on tatami mats, too. Some mega ryokans have pretty good buffets/'vikings' for dinner which don't involve the tatami experience. Still advisable to wear ryokan with undergarments and the proper foot wear. Going to a ryokan buffet in western dress is unusual, in my experience.