Lighter (evidently following P. Tamony, Americanisms, no. 7, 1965) derives it from the phrase "have a life," apparently a chant heard in baseball fields in the 1930s. Lighter's first citation (habba habba) stems from 1941, which would exclude an origin from servicemen in North Africa, where we did not intervene until 1942. Otherwise knowledge of Arabic was quite sparse in the US in those days.
The term (including its extended meaning of sexual admiration) was popular among servicemen in the Pacific theater during WWII. Hence the claim that it might be Micronesian, which seems quite unlikely.
The duplication is relatively uncommon in English. Cf. however "dumb dumb" (originally spelled dum dum, reflecting the homonymous bullets, derived from a fortress in India). Note also: bang bang. One of Pauline Kael's collections was entitled "Kiss kiss, bang bang." The kiss-kiss duplication seems to be a personal contribution. Likewise the Churchillian "Better jaw-jaw than war-war." Yak-yak-yak is triple, while a related form may be either double or triple: yadda yadda or yadda yadda yadda (popularized by the Seinfeld TV show, but originally British). Duplication is ubiquitous in Malay and Bahasa Indonesia, where it serves to create plurals (eg. orang, man; orang orang, men). There seem to be no comparable expressions in those languages. At all events an exotic source is required.
After going underground for several decades the expression hubba hubba seems to have resurfaced in popular-entertainment media in the 1980s (e.g. Pee-Wee's Playhouse, CBS-TV, 1988). There is now a leather goods shop of that name in Cambridge, MA; a band; and a tent—all using that name.
In New Zealand the government sponsors a campaign for sexual responsibility called "No rubba, no hubba hubba." Here the expression clearly refers to the sexual act itself.
Somehow, though the exclamation "hubba hubba!" s o u n d s exotic, a quality which may serve as an acceptable mask for the lust encapsulated in its common usage. "F*cky f*cky!" would be downright rude.
On a somewhat different note, I recently skimmed a little bagatelle book published by Princeton University Press, entitled "On Bullshit," by the philosopher Harry Frankfurt. In a nutshell "bullshit" may defined as pretension talk featuring untruths or exaggerations that the speaker knows to be such. It may also refer to evasions, as in the expression "Don't bullshit me.
Commenting on the lack of scholarly literature (!) on the subject, Frankfurt does mention a book by another philosopher, Max Black, which deals with a closely related phenomenon, humbug. Perhaps humbug serves as a kind of euphemism substituting in situations where bullshit would be unacceptable.
Frankfurt believes that the incidence of bullshit has increased nowadays. The relativism promoted by postmodernism has blurred the boundary between statements that are true and objective and contetable, subjective one's. In a sense, bullshit is now (in this view) impossible: when everything is b.s., nothing is.
Instead of making comments about the world, the postmodernist increasingly turns to making statements about his or herself. But we cannot know ourselves with any accuracy. But we can endlessly emit b.s. about it.