Use (FreeBSD) native log shipping instead of Filebeat?

It heavily depends on your setup. If you just run one server and you need Logstash, there is no need for filebeat and you can directly use Logstash. If you have several servers and a central Logstash instance, the small and lightweight filebeat instance on each server makes sense.

There is also a wide variety of plugins in Logstash to connect some standard systems like syslog: https://www.elastic.co/guide/en/logstash/current/input-plugins.html

There is no "one solution fits all". Best is to let us know what your limitations are and your setup to give some better insights. But experimenting is probably in the end the best way to figure out what fits your environment best.