The instances of Emma as a "male" name in the late 19th/early 20th c. are almost certainly due to recording errors. See http://www.socialsecurity.gov/OACT/babynames/background.html
, #2 under "data qualifications."
Because of these recording errors, many male and female names can be found on the top 1000 list for the opposite sex during the times they were very popular. For example, Jennifer makes the top 1000 as a "male" name from 1967 to 1989; ditto Thomas as a "female" name through much of the 20th c.