After immigrants are detained by ICE, there are probably records somewhere of who has an attorney, and who is calling family members or an attorney.
For the immigrants who aren't calling any family or lawyers, the poorest of the poor, people with little to no connection to anyone, who may not even say which country they are from, if the administration were actually trying to kill as many disconnected immigrants as possible in secret, would society know?
For example, if the administration was composed of all types of conservative people, but 30 percent were secretly Nazis or wanted racial genocide, could there be a campaign to not just remove, but kill, immigrants, and the public doesn't find out?
Bodies. While possible, disposing of that many bodies without anyone noticing will be really hard.
They're already using military cargo planes for "deportation" flights. Maybe some don't have any live passengers, and they just dump the bodies mid-ocean. No need for mass graves, just load cargo containers onto a cargo plane and off it goes. If it lands with one or two fewer than it started with, that's just a paperwork issue.