This is a difficult question to address because we simply don't have information about their intimate life; however, we can certainly speculate...

John, to me, is not a likeable character, although his actions were perhaps typical of a male during this time period as it relates to getting treatment for his wife.  He was a doctor and perhaps, deep down, he felt he was doing what was best for his wife.  Clearly, there is a lack of communication with the couple.  The narrator wasn't able to protest too much about her treatment and only discussed it in her journal.  It wasn't her "place" to do so as a woman.  Because she wasn't able to be open with her husband, her mental health suffered, and in the end, suffered greatly. Had John been willing to listen to the narrator's feelings and what SHE felt was best for dealing with her depression, things might have turned out differently.

As for John having an affair, I've always had this suspicion since the first time I read this story many years ago.  I've never trusted John and I've always had the impression that he was a shady character and that he was having an affair.