The reason for having those pieces of software in the base system is that they're deemed important enough that many (or even most) users will benefit from them being available out of the box, without having to download additional software. For example, almost everybody will need ssh. There are also some cases where a piece of software is kept for historical reasons or “BSD tradition”. For example, sendmail has been part of BSD UNIX for almost 40 years.
Such software is usually also available from the Ports Collection (and as binary packages). The reason for that is that the versions included in the base system are often stripped down and somewhat limited. For example, the version of ntpd included in the base system is perfectly fine to be used as a client or simple server. However, the version of ntpd in the Ports Collection includes wider support for various kinds of hardware reference clocks, and it supports SNMP and a few other things that most people won't need. Also, software in the Ports Collection is easier to update, so it is often a newer version than the one in the base system.