In its Shakspearian bearing may have meant secretly, or in a clandestine manner, but its nautical application is to express anything out of order or done in a slovenly way.
·adj Secret; clandestine; sly. II. Hugger-mugger ·adj Confused; disorderly; slovenly; mean; as, hug...
Webster's Dictionary of the English Language
By stealth, privately, without making an appearance. They spent their money in a hugger mugger way. ...
Dictionary of The Vulgar Tongue by Francis Grose
·noun One who hugs or embraces. II. Hugger ·vt & ·vi To <<Conceal>>; to lurk ambush. ...
·add. ·- ·Alt. of <<Muggur>>. ...