Some of your concerns are addressed in the wiki on freeread.org: http://freeread.org/reddit-libgen/

VirusTotal includes some very poor quality Chinese AVs that produce positives for nearly every file. PDFs are pretty damn safe to access today -- the days of exploding macro exploits are about a decade behind us.

Yes it's just ebooks.

Even an ordinary .PDF can have executable content. This isn't a baseless concern.

and scientific papers

what red flags did you see?

It was some book, and when submitting the download link, 3 of the antivirus results were red. Perhaps they were false positives.

Anti-Virus tools have been flagging keygens and cracks for ages, and also hacking tools that grab passwords from (system) stores even if the tools have absolutely nothing in their code that talks to a server (I only ever used those for legal purposes, but can't tell you how often I had to disable an annoying AV...). Just because the AV says something is malware doesn't mean you can trust its claim. From my perspective, they've undermined their trustworthiness in the area where you are indeed most likely to rely on an AV.

I'm not surprised they're now flagging what is basically text and images as malware.