'The tusk, especially the tip of the tusk, was used to interrogate and manipulate the target by brief contact, which typically elicited a response from the fish.'
Well, yes, if you were poked by one of those tusks you'd react!
In my native language it carries the context of semi-forcibly extracting information from someone, and English dictionaries seem to suggest the same meaning, but I see it used in literature and academic contexts in many ways that don't fit that definition. What am I missing?
As far as I am aware, this is not a common usage, and you could go a very long time before you encounter it again. Next time you encounter it will probably be on Hacker News.
Edit: After thinking about it some more, I believe probe and interrogate are closely related. Essentially, an interrogation consists of a number of probes for the purpose of discovery. Normally, we think of an interrogation as being verbal, but in this case the interrogation is physical and consisting of a series of probing movements.
In a typical verbal interrogation, the investigator or detective will ask probing questions.
It’s definitely a less common usage but as you say it has the sense of questing or probing or feeling out. For me it belongs to a higher register of language, it’s a word I might use in that sense when writing a report or a formal email or something of that nature.