In Acrobat Pro, you can select the target PDF version for each document
type that you convert. We have selected to convert all of our documents
to v1.4, which can be read in Reader 5.0 and later and indexed with
iFilter 5.0 and later. Some of the new PDF features require newer
versions, so some publishers will no doubt be creating PDFs in these new
formats. So, depending upon how much control you have over the PDF
documents in your repository (Are they coming in from outside? Can you
negotiate which version your authors produce their documents in?), you
may or may not have a problem.
When we ran iFilter 5.0, documents arriving from outside and produced
with Acrobat 6.0 (PDF 1.5) would not index. I expect that your first
document produced using PDF 1.6 will not index with iFilter 6.0.