Quite honestly, I think the behavior is on the highest order of jerkishness. A nice request could be done in the documentation, instead the path chosen is to bully users of the software.
Once more, because it is free software, we are free to use it despite what Ole thinks. We are free to patch it out too.
Why? Whether something has contributed meaningfully to my research is my decision, not Ole's. Not having light "hinders my science", so I'll be sure to cite Edison on all my papers.
I agree with the sibling commentator that Ole's behavior is jerkish. Not because he asked for citations, but that he misleads users by claiming his request is standard, when it is decidedly not. He also obfuscates the voluntary nature of his request as much as possible, to make it seem like citing is a legal requirement. And he is inflammatory in responding to people who make the perfectly valid decision to not cite him, or to patch the notice out.
The Golden Rule.
You would be pissed if you spent years on something, felt it was a contribution, saw the community use it, asked them to cite it, and weren't cited.
Whether or not it's standard is irrelevant. Ole asked you to cite him if you use it. So, if you publish academically, either don't use it or cite him. If not using GNU Parallel hinders your science then the tool must be material to your work flows.
For comparison, how many dumb citations do people add to their papers that point to marginally relevant work coming out of the same research center or academic lineage? Those aren't scientifically relevant but they are standard. Let's not pretend the academy is full of citation purists.