Without knowing what aspects of Upton's life you are researching and where you are in that research, it's a bit difficult to help you in your efforts. You may be aware of Terry Foenander, a highly respected and very well known Naval historian and researcher. Here is the url address for his list of microfilms of Civil War era Naval courts martial available through the National Archives: http://www.oocities.org/tfoenander/courtsmartial.htm This list was compiled in 2001. Transcripts of the Upton proceedings may have become available since then. I don't know which of the two courts martial is of particular interest to you.
I am aware of other sources of information regarding Upton, but, again, I don't know what you are looking for.
As for Lt. Commander Hart, I don't believe his suicide has any connection to Upton's. There is a great deal of information on these forums covering the events that led to the first of Upton's courts martial, for failing to assist the Albatross off Fort DeRussy.
I wish you luck with your project and I am sorry I can't be more helpful.