The choice to never name Tom's second yeerk is such a fascinating move. There were plenty of points in 53 where Applegate could have dropped it. The deal with Jake. Have Visser One address him by name.
But she never names him. He's always "Tom's Yeerk." Or, more horrifyingly, just shortened to "Tom" for the sake of brevity.
We even know that Jake knows the yeerk's name:
Nervous, toadying laughter all around. Someone reported that Tom had reached the Blade ship. The Blade ship was reporting readiness to join the attack.
Whoever reported this definitely didn't call him Tom.
But Jake never uses it. Neither does Rachel.
There is no separating Jake's trapped brother from the yeerk controlling him by using his name as a euphemism for the person Rachel is sent to kill.