Somehow, between the beginning of the Linux era and, say, 2005 or so, people forgot how to efficiently comprehend large assembly programs. But it's not 2005 anymore; it's fully ten years later. Virtually every software security team in the world has multiple people on staff who know what basic blocks and control flow graphs are. There are credible open-source competitors to IDA, and arguably the best disassembler currently available costs something like $80 and backs assembly out to C.
Closed source software imposes meaningful, significant costs. It's reasonable to prefer open-source code, or even to require it. But we cannot reasonably make the excuse that closed-source code is a "black box" anymore.