Good idea replacing them all. I can't believe they could get so bad and I would trust anything that looked OK.
Sorry I don't know what Knees are. I presume this is where the plate bolts to the Hull
??? Yes I would go a larger bolt. But don't just make it snug. Drill the hole to ensure you get all the elongation out. This is important to enable a good surface contact with the bolt. The bolt needs to be of snug fit to stop any chance of movement. Movement causes wear and elongation once again. Once you have settled on a drill size to ensure a good clean hole, then use a bolt that suits the hole diameter. You may want to ensure you can get a bolt for the size you drill prior to drilling of course.
I also would be looking at a slightly heavier chain plate
material. Preferably wider, which would better suit the new larger diameter holes. But those old ones should not just crack like that.