K.S.
If your baby will take the silicone paci that's great. If he will only take latex, I would not stress about it. Just replace pacis that seem to be deteriorating. Hopefully your child will only use pacis for a couple years of his life, so I do not think the latex will cause any damage.
You can get a product called Grapefruit Seed Extract from Whole Foods. Just use a couple drops of it in water, and you can soak the pacis for about 2 hours. I don't recall how it worked with latex, but it cleans without any toxins that can come from soap. I would opt to do that before I would loose the latex.