True. It preflights the original PDF and writes out a new file. The text in question is still selectable (not vectorised or rasterised) text in the PDF it outputs. Are there any special criteria for text that can't be made into links by Acrobat/Reader?
I have created a couple of examples that illustrate the problem - that might help pinpoint exactly where the problem is occurring - https://www.dropbox.com/s/ltqxcht9ydgh9or/examples.zip. The "proper" hyperlink (created in ID) doesn't survive the process, which I expected. The web address at the bottom of the advert is not a proper hyperlink (it stops working if you turn off the "Create links out of URLs" option) but works in the before file but not the after.