ArcMap does not support transparency when exporting to EPS, PDF, or AI formats. To preserve the visual effect of layer transparency, ArcMap exports transparent vector map layers as raster. EPS and the PostScript language, as well as the documented versions of the AI format, do not support definition of transparency on vector graphics.
Exporting transparency is now supported in ArcGIS Pro.
Starting from ArcMap 10.5, Production PDF allows transferring layer level transparency from feature layers in ArcMap to PDF layers. This is supported when 'Export PDF Layers Only' or 'Export PDF Layers and Feature Attributes' under the Advanced tab is enabled. Advanced field base (feature level) transparency is not supported, even when this is enabled.
Note: Production PDF is available with Production Mapping license.