See if this helps with the Illustrator part of your question:
Losing large portions of elevation contours from QGIS to PDF
Short answer on QGIS layers to PDF layers support, not yet. My guess would be some form of support might show up by way of the GDAL/OGR providers.
While the version 2 GDAL driver and OGR driver have model-tree layer support for writing PDFs, it's not the same as 'regular' PDF layers.
Sample of Model-Tree (not produced with GDAL/OGR)
The GDAL driver appears to have support for layering an OGR data source over a raster layer (see OGR_DATASOURCE).
Here is some recent discussion on the subject:
GDAL - Dev - [gdal-dev] Geospatial PDF with OGR_DATASOURCE
And some discussion on regular PDF layer support:
GDAL - Dev - [gdal-dev] PDF selective layer sample wanted
There are other libraries, like Cairo and Poppler, but I don't know if anyone is integrating them with QGIS.