The unfortunate answer is, it depends..
Using FreeBSD 10 as an example, all the packages are currently built on 10.3. If you look at /usr/ports/Mk/bsd.default-versions.mk you'll see the default versions for a large number of ports.
Now here's where it becomes an issue.
The other day I installed mysql5.7, nginx & php7.1 from pkg. No problem. However, when it came to installing pear (which I needed for a specific application), the port relies on php. Because the packages are currently built with php5.6 as the default version, it was built against php5.6 and wanted to remove php7.1 and install php5.6 instead.
While I was perfectly able to install php7.1 from packages, I had to override the default php version by adding DEFAULT_VERSIONS += php=7.1
to /etc/make.conf and build pear by hand (using the port). There would be no way to install the official package without it demanding I use php5.6.
So basically, in general there's no issue with mixing ports and packages. When you install a port all that happens is you locally create the package, and then install that package. However you may see issues when you install a package or port that depends on something else you've already installed, and the version the package/port depends on is not the version you installed.