I don't think I would use scotchguard, because of concerns of all of those chemicals. I know there are waterproofing sprays designed for clothing items available, but I have avoided them for the same reason. To me it just goes against the reasons I cd.
I have had diapers that stopped working. If, after a good stripping, they still leak or wick, I just chalk it up to the fact that diapers only last so long, and they have done their duty and it's time to replace them.