We've encountered a similar problem. We create a number of small INDD files (1-4 pages) that contain hyperlinks to various websites. The smaller files are then placed (File - Place) into larger INDD files. The larger INDD files are collected into a Book, and the Book is exported to a (print) PDF, with the options checked for Hyperlinks, and Tagged PDF. In the Book PDF, the hyperlinks are no longer functional (although a few have a very truncated link, such as "http://www"). The PDF also has NO functional tags, although that's not an issue for us. (In earlier versions, we had to create a tagged PDF in order for the hyperlinks to be carried over into the Book PDF.) If the Book is exported to an Interactive PDF, tags are generated, but the hyperlinks in the placed files still don't work.
If the smaller files are exported to PDF directly, most if not all, of the links are active in the smaller PDF.
The most frustrating part is that these links WORKED in previous versions of InDesign, for that last 3-5 years. The only thing that has changed is InDesign--we just upgraded to 17.0.1x64 (Windows).
This is a huge problem, as we now have to manually (re)create more than a dozen links every time we generate a PDF from the Book. These are high-profile reports, and the manual linking always introduces the possibility of errors.

@swapan The links do not show up in the interactive panel. I believe this would be correct based on your statement, IndDesign doesn't treat as a PDF/Text but and Object.... On output the pdf text is flawless so it is most definitely and object, the object gets manipulated and strips the links out on output. Just seems to me there should be a way to allow these links to stay... I don't believe this has worked in other versions in the past.

Not sure whether this features is available on placed object. Indesign treat this as an object/image not an text. Thus not creating any links. Is this feature available earlier? Please do check in Interactive->hyperlink