I've been on an Amtrak train that went into emergency, after it hit a pile of stuff stacked on the tracks under an overcrossing, probably at 79-80mph, and some of the trash bounced off the side slopes or abutments, got under the cars, and tore the brake line off one of them. There was a long wait for a fix (out in the country, no nearby roads) while we blocked the BNSF single-track line. We did not get flat wheels, as was apparent once we got going again at reduced speed (though the train was taken out of service at the next station and those going farther had to get on a bus; luckily, it was my station).

I've also been on light rail trains that go into emergency, on Sacramento RT. The old Siemens cars could in fact get flat spots from a high-speed emergency stop. The newer CAF cars apparently have effective anti-slip, and very few have flat spots, from emergency stops or otherwise.