Board Thread:General Discussion/@comment-10941901-20130628153213/@comment-4913740-20130628164246

I wish we could clear this up once and for all, but it keeps resurfacing.

Jack has been pointed out to be another name for John. The Boss calls him Jack because they're close. Zero will call him Jack over the CODEC in the beginning IF you chose the "I liked MGS2!" option. This was to make a reference to MGS2, along with the mask, giving the illusion of playing as Jack, codenamed Raiden. Since Raiden's real name is Jack, having Big Boss share the same name would be rather confusing.

The MGS4 database, while fairly inaccurate in some areas, has fairly accurate information in other areas. And it states his name is John. Just like it states that Solid Snake's real name is David, and Otacon's is Hal, etc.

And of course, the above wikia contributor stated that Zadornov also calls him John in Peace Walker.

The smiling might be because, again like the wikia contributor above stated, he is touched that Ocelot wants to know what Snake's name is, to see them as equals.