I am unable to reproduce the crash under 1.2.8 or my latest internal beta, granted I don't use Windows 8, but ZDE was tested under Windows 10, which shares a lot of 8's awful DNA. Though it is weird, I'm glad it's working for you.
What happens if you go to Options -> Paths (can be accessed by pressing F5 as well) and click Ok?
As for hard links...
https://en.wikipedia.org/wiki/Hard_link
Given their nature, ZDE should have no problems handling them (and I do recall all the IWADs I handled with ZDE were hardlinks at some point for convenience, specially when testing under FreeBSD, since data duplication is rather pointless), but it was just an example that came to mind that could illustrate kind-of out of the ordinary setups. A couple of other odd setups that could come to mind:
-IWADs flushed to a folder and then telling ZDE the folder's an IWAD (I haven't tested this, but it could, indeed, kill ZDE as it expects IWADs or PK3 files).
-if such a thing exists, something that makes Windows treat IWADs like folders every single time (same reason as above if the program really, really hooks into Windows).
-Though those really shouldn't be a problem, some kind of tampered with IWADs.
Edit: Ok, here's something that just occurred to me: as of right now, just selecting an IWADs path doesn't automagically fill the IWADs under the IWADs tab in the setup screen, it doesn't crash (nor should it) the program if they're not filled (I just re-tested), but maybe that is related, given the description you gave?