No one is sure.

1) Admiral Josephus Daniels imposed a ban on serving alchoholic drinks on Navy ships. Coffee became a very popular drink as a result, and was so named after the Admiral who imposed the ban (supposedly).

2)

A) Admiral Josephus “Joe” Daniels, Secretary of the Navy (1912-20)
B) a modification of java or jamoke for coffee

yes. that was correct...

Ever had a "Cup of Joe"? Secretary of the Navy Josephus Daniels, scandalized by reports of drunkenness aboard ship, issued an order in 1919 banning the serving of wine in the wardroom and any consumption of alcohol aboard ship. Daniels, a teetotaler, decreed that only coffee or tea should be served. This was not a popular order and Sailors promptly dubbed a cup of coffee as a "cup of joe."