For what it's worth, I've never seen an accusation that the banking system in Nigeria is itself materially involved with advance-fee scams or otherwise corrupt, and I don't have the impression that people believe that. I took "into a Nigerian bank account" as shorthand for "unexpectedly into the custody of Nigerian internet users", and the unfortunate stereotype persists around the guys hanging around internet cafes, not the bankers. Just as "into a Swiss bank account" connotes money that is being made more difficult to trace, not a criticism of people in Switzerland who actually operate the banks.