It seems like half this novel takes place at night. The Patna sinks at night, Jim confesses his shameful actions to Marlow under the cover of darkness, Marlow relates his story to an audience over the course of a night, and a lot of Jim's exciting Patusan adventures occur after the sun goes down. So what's the deal with the darkness?
Of course it's more dangerous, exciting, and suspenseful than daytime. But more than that, it conceals things. Things like secrets.
A huge chunk of Lord Jim deals with people sharing secrets, and having them do so in darkness emphasizes the clandestine nature of their conversations. Some secrets are hard to fully discover, too, which is yet another thing that darkness symbolizes in Lord Jim. Marlow frequently notes that Jim was obscured from him, like the moment in Chapter 16, when he says, "He was not—if I may say so—clear to me" (16.2). It makes sense that Marlow speaks of Jim at night, when it's hard to see clearly, and facial expressions remain in shadows.