The primary meaning is clandestinely. The secondary meaning is disorderly, in a slovenly manner. To hugger is to lie in ambush, from the Danish hug, huger, huggring, to squat on the ground; mugger is the Danish smug, clandestinely, whence our word smuggle.
The king in Hamlet says of Polonius: “We have done but greenly in hugger-mugger to inter him” —i.e. to smuggle him into the grave clandestinely and without ceremony.
Sir T. North, in his Plutarch, says: “Antonius thought that his body should be honourably buried, and not in hugger-mugger” (clandestinely).
While I, in hugger-mugger hid, Have noted all they said and did.
Under the secondary idea we have the following expressions: He lives in a hugger-mugger sort of way; the rooms were all hugger-mugger (disorderly).
Source: Dictionary of Phrase and Fable, E. Cobham Brewer, 1894