> How is Nintendo's "establish communication and clarify that nothing illegal is going on" any different from a lawyer sending a cease-and-desist?

I am unsure about how it works in your jurisdiction, but where I live, sending a C&D rarely involves a lawyer sitting outside your house to note your schedule as well as other comings and goings.

I can see exactly how this has played out:

1) Someone at Nintendo learns about a "anonymous hacker conducting exploits against the 3DS"

2) Exec's panic because "anonymous hacker" and a history of piracy battles and consequently hire a private eye to find out about the person behind the exploiting

3) Private eye does their job and writes a detailed report in the style of a private eye

4) Nintendo uses information to establish communications with said hacker

Just Hanlon's razor at work