PDF is an older format, which follows an international standard. It has not and probably never will give that kind of support for HTML.
You could look to DPS or EPUB3 workflows instead.
I'm not familiar with the DPS or EPUB3 workflows, but will start researching them.
One question though: Will either of those workflows support desktops or just mobile devices?
My Agency creates massive directory publications that are published in print and also in PDF form on our website. I'm thinking that most of the users who access these directories would be from desktop office computers.
Thanks for your help.
DPS = Adobe Digital Publishing Suite. Used in apps for tablets or smartphones.
EPUB3 = A format for eBooks. InDesign CS6 doesn't provide the latest support for EPUB3 export. There have been big improvements in InDesign CC, including creating Fixed Format EPUB. EPUB3 would be supported by a variety of EPUB supporting applications and within browsers on both desktop, tablets/smartphones and dedicated EPUB devices.