As far as I can tell, there is no tool in FreeBSD base that provides a simple way to check and update all ports using binaries. FreeBSD's pkg_add only handles direct installs of new packages. Upgrade management, things like "update everything" or "update this package and its dependencies" is usually done through one of the external tools like portmaster, portupgrade, pkg_upgrade, etc. Which interact with the ports tree and pkg_add behind the scenes, but with additional info on dependencies to keep the whole thing sane. They do the job okay, but they all have their quirks.

From its man page, it seems OpenBSD's pkg_add supports updating (and a lot of other things), so I guess they don't have this problem to start with. That's interesting, I wonder why the feature is lacking on the FreeBSD side.