Combine onions, soy sauce, and sugar in bowl and microwave until just softened, about 5 minutes, stirring halfway through cooking. Spread onions and their liquid in bottom of slow cooker. Arrange bratwursts in single layer on top of onions.
Whisk beer, mustard, and caraway seeds together in bowl and add to slow cooker. Cover and cook until bratwursts are tender, 6 to 8 hours on low or 4 hours on high.
Transfer bratwursts to platter and tent loosely with aluminum foil. Stir sauerkraut into onion mixture in slow cooker and let sit until warmed through, about 5 minutes. Strain onion-sauerkraut mixture through colander, discarding liquid, and transfer to serving bowl. Serve bratwursts on rolls, topped with onion-sauerkraut mixture and mustard.