pkg_delete is more reliable. It uses the info stored under /var/db/pkg/portname-version. This is the info that was stored when the port was installed, and most accurately describes what's installed and where.
make deinstall uses what's in the ports Makefile to determine what to delete. However, if you have updated your ports tree since installing the original app, the info in the port directory may be different from what's actually installed on disk. For example, you may have installed version X of the app, but the ports tree has the info for version X+3 of the app.
Use the ports tree to install and update software, but use the pkg_* tools to manipulate installed apps.
