Has the North Korean leader ever visited the JSA?

Sure. This report from CNN shows Kim Jong-un in the JSA in 2012. If you watch the video, the balcony that Kim and Co. are standing on at the 27 and 40 second marks are on the third floor of Panmungak on the northern side of the border.

From North Korean Leader Watch there is some more information about that visit, as well as one of Kim Jong-il visiting in 1996.

Really, visiting the JSA is no big deal. I've been there twice. I took my parents there.

Even during the Armistice talks, Kim Il-sung and Syngman Rhee didn't go to the actual meetings. When the documents were signed, Kim signed in Kaeseong, 10km away, and Mark Clark, commander of the UNC forces signed in Munsan, about 10km in the other direction.

A better question is what has been the most significant meeting that has taken place there, and who is the highest ranking North Korean leader to have participated in meetings at the JSA? Unfortunately, it's still not a very interesting answer.

From the end of the war until the early 1970's, there was virtually no contact between the northern and southern governments, and especially NOT at the JSA. The JSA is a VERY public place - the North and the South are there, as well as the UNMAC - UN Military Armistice Commission - made up of observers from "free" and "communist" countries at the time. If anyone of importance were to show up at the JSA, word would get out.

The 1972 North South Join Statement came about via secret communications. The head of the KCIA (South) went to Pyongyang and the deputy premier (North) went to Seoul. As a result, a hotline was set up between the two governments. Throughout the 70's, a series of meetings were held on reunification issues.

Since then, there have been other meetings - Korean Red Cross meetings on family visits, military meetings, other inter-governmental meetings - but none of them have had anything higher than a Ministerial level leader. In the early 90's, when the UNC appointed a South Korean general as their representative, the North Koreans pulled out of MAC (Military Armistice Commission) meetings because officially, South Korea was not a signatory to the Armistice, they couldn't participate, so even the basic day-to-day meetings became pretty rare.

Roh Moo-hyun, the South Korean president walked across the DMZ on his way to the Second Inter-Korean summit in 2007 but this was more symbolic than anything - Kim Jong-il didn't meet him there, the actual summit was in Pyongyang, and he walked across on the actual highway, not in the JSA.

The most important meetings that have happened at the JSA? That's a tough call. People are exchanged there - POW's during Operation Little/Big Switch, fishermen that have drifted over the NLL, corpses of agents killed, remains of bodies from the war. I'd say that this is a really subjective question and just leave it by saying that most meetings at the JSA are fairly innocuous and that important meetings between the North and South happen in Seoul or Pyongyang, or in secret, in third countries.

TLDR - yes, North Korean leaders have gone to the JSA. South Korean leaders have gone there, too. However, no meetings between these leaders have happened there. Further, the most significant meetings have always happened outside of the JSA. Meetings that happen in the JSA tend to be symbolic or working level meetings to hammer out details for agreements arranged elsewhere.