EPS is a vector format, which means it's a mathematical description of the graph or diagram. This can be edited automatically, for example a script can change all the colours in the graph to shades of gray. EPS figures can be scaled to any size without loss of resolution.
PDF can include vector graphics, in the EPS or other formats, but it can also include raster images, which can not so easily be edited by scripts, and is problematic to scale to different sizes. If the submitter submits a PDF graph, which might display and print beautifully on their computer, it might be either a raster image or a vector image, and the publisher has no way to tell without opening the PDF.
Most authors don't know if the software they use produce vector-based or raster-based PDF images. For all they know their PDF of a beautiful graph might be an embedded Flash image. It will print beautifully, but it will not fit into the publisher's workflow.
The only way for a publisher to ensure they get a vector image is to require a vector format. In future they might switch to SVG or a more modern vector format, but for the moment EPS is still widely supported.
In summary: while PDF is a perfectly good format to submit to printers, it can easily cause problems to editors (and their technical staff), so for the moment they demand EPS.