I presume they mean nginx will be the default web server, rather than removing Apache altogether? You can't just replace Apache with nginx, they're two different pieces of software - admittedly with some overlap.
It says "to provide an apache replacement for base." OpenBSD has a Base system, plus it has Packages and Ports. Packages and Ports do not go through the same security audit as the Base system. Currently the version of httpd in Base is 1.3.x, which is all patched and secure, Packages/Ports has httpd 2.2.x. I suspect they mean nginx will replace httpd in the Base system, while httpd will still be in Packages/Ports.
On Linux distributions, all software is typically "equal" - everything is a package, and the only difference is what repository it comes from.
In BSD, the base system and ports are entirely distinct. The base system is a single coherent unit installed and upgraded as one piece (although the installer allows you to omit some portions of it).
The ports provide additional software packages installed and managed separately on top of the base system. The base system is maintained and patched by the core developers and officially supported by the organization. The ports are provided effectively as a convenience, and are not covered by the same security and maintenance procedures as the base system.