Судя по всему правильный ответ: они забьют на пакеты которые не считают "серверными"
Are there different repositories for desktop and server?
No, there are no desktop- and server-specific repositories. This means that you can install server packages on an Ubuntu Desktop installation as well as on an Ubuntu Server installation.
How does the package system (apt) know what to install or update (server or desktop packages)?
It doesn't. The sysadmin should know what he/she is installing. When upgrading/updating packages (apt-get update && apt-get upgrade), apt will update only the packages already installed on the system.
There are also some packages available to automate the process. One is apticron a cron script that will email an administrator with details about which packages are ready for updating. The unattended-upgrades package can be configured to automatically install security updates, or all updates.