Googleando un poco he encontrado una interesantísima
comparación entre los kernels server y desktop de Ubuntu. En el último párrafo se explica eso de los Hz del kernel:
Cita: The server kernel is set to a timer interrupt rate of 100 Hz (CONFIG_HZ=100, CONFIG_HZ_100=y), which means it accepts 100 interrupts per second. Another way to think of this is the kernel looks up and peers around 100 times per second for something to do. The desktop kernel is set to 250 Hz; lower numbers = lower overhead and higher latency, higher numbers = higher overhead and lower latency. Higher numbers generally mean the system feels more responsive, at the price of higher CPU usage. Some processes require more interrupts; for example, video processing and VoIP servers need 1000 Hz. If you need to change the Hz value it requires a kernel re-compile.
Parecer ser que de esta manera la versión "server" sacrifica velocidad de respuesta a cambio de un uso más eficiente de la capacidad de proceso.