If NAFTA falls apart, how would this affect the railroads? Would CN and CP have to break up their American holdings? What about KCS?
No. Or at least extremely doubtful. Corporate ownership across international borders is not exactly a trade issue, and multi-national companies pre-date the original NAFTA by decades.
Now, business operations could be affected in a myriad of ways. But for railroads, that would probably be mostly through levels of traffic.