How easy is it for automated tools to spot encryption routines in a binary? If my notepad replacement had call to encryption algorithms in it I'd be a bit surprised...
Many crypto routines have identifiable constants but there are myriad ways to obfuscate code too so I'm not sure there's an answer other than: It depends on how hard they're trying to avoid you and how hard you're trying to find them.
I think the problem is then to avoid punishing binaries for, e.g., using a hashmap :)