He might, it will take a lot of focus at first. He would probably be detecting a good and evil within John, sort of colliding. Duo would be HIGHLY cautious of John at first before realizing what is going on. Since Duo has the ability to purge evil from one's body he might be able to get Ansem out of John quite possibly (though that would be up to Katrix.)
Duo never really is "uncomfortable" near people, even when they are filled with evil or have an evil presence. After all Duo shows little to no emotions (though he does experience some emotions.) He would be cautious around HM, even more so than John as Duo would be able to easily detect the evil within HM. Unlike John who has Ansem inside him which is causing the detection of two people and two energies, one good and one bad.
Ikr? It also serves not just as his normal theme, but as his battle theme as well.
Something about it just screams a just person. Someone who is against all that is evil, but yet one who is distant from others. Sort of a lone wolf kind of deal.