These are all interrogative words so there is nothing weird that they all share the same prefix "wh".
And actually there are more than 600 English words that start with "wh", even there is a history for "wh", there won't exist a strong connection between that history and the set of interrogative words.
From Wikipedia:
Early history of ‹wh›
What is now English ‹wh› originated as the Proto-Indo-European consonant *kʷ. As a result of Grimm's Law, Indo-European voiceless stops became voiceless fricatives in most environments in Germanic languages. Thus the labialized velar stop *kʷ initially became presumably a labialized velar fricative *xʷ in pre-Proto-Germanic, then probably becoming *[ʍ] in Proto-Germanic proper. The sound was used in Gothic and represented by the symbol known as hwair; in Old English it was spelled as ‹hw›. The spelling was changed to ‹wh› in Middle English, but it retained the pronunciation [ʍ], in some dialects as late as the present day.
Because Proto-Indo-European interrogative words typically began with *kʷ, English interrogative words (such as who, which, what, when, where) typically begin with ‹wh›. As a result of this tendency, a common grammatical phenomenon affecting interrogative words has been given the name wh-movement, even in reference to languages in which interrogative words do not begin with ‹wh›.
Edit: found the citation from 1672, from Andrew Marvell’s The Rehearsal Transpros'd:
Two or three brawny Fellows in a
Corner, with meer Ink and
Elbow-grease, do more Harm than an
Hundred systematical Divines with
their sweaty Preaching.
It's also defined in B.E.'s A New Dictionary of the Terms Ancient and Modern of the Canting Crew, in its several tribes, of gypsies, beggers, thieves, cheats, &c. with an addition of some proverbs, phrases, figurative speeches, &c., c.1698:
Elbow-greaſe, a deriſory term for
Sweat. It will coſt nothing but a
little Elbow-grease ; in a jeer to one
that is lazy, and thinks much of his
Labour.
I found no earlier mentions than senderle, but here are some useful references. These are the earliest references I could find, and helpfully, they are also dictionary definitions.
The Online Etymology Dictionary says
Phrase elbow grease "hard rubbing" is
attested from 1670s, from jocular
sense of "the best substance for
polishing furniture."
There's a similarly colourful definition in Francis Grose's 1785 A Classical Dictionary of the Vulgar Tongue:
ELBOW GREASE, labour, elbow grease
will make an oak table shine.
(The rest of this dictionary is interesting too!)
Also, very pertinent to the question, here's The Royal Dictionary, French and English, and English and French by Abel Boyer in 1729:
Elbow-grease, (or Pains) Rude travail.
Rude travail is French for rough work. There's no entry for "l'huile de coude" in the French side.
And in John S. Farmer and W.E. Henley's 1905 A Dictionary of Slang and Colloquial English:
Elbow-grease. Energetic and continuous
manual labour : e.g. Elbow-grease is
the best furniture oil : Fr., huile de
bras or de poignet ; du foulage
(1779).
French huile de bras or de poignet is oil of the arm, wrist which is quite close. I think du foulage is fulling, the manual scouring and milling of cloth.
The earliest French reference I could "l'huile de coude" helpfully explains the term. In Jean Humbert's 1852 Nouveau Glossaire Genevois: Volume 1 (New Geneva Glossary):
Dans le langage badin des domestiques
et des maîtresses, l'huile de coude,
c'est le frottage, c'est-à-dire : Le
travail de la servante qui frotte.
Ces meubles, Madame, ne veulent pas
devenir brillants. — C'est que, ma
mie, tu y as sans doute économisé
l'huile de coude; c'est-à-dire : Tu as
trop ménagé ton bras et tes forces.
A rough translation:
In the playful language of servants
and masters, elbow grease is rubbing,
i.e. the work of the maid
who scrubs. This furniture, Madam,
does not want to shine. - My dear,
that is because you have undoubtedly
skimped on the elbow grease. In other
words, you have conserved both your arm and
your strength.
These references also suggest that "l'huile de coude" is an anglicisme.
Best Answer
Origin of the usage
A Google Books search for "Look who it ain't" turns up 21 unique matches, the earliest of which are from the 1960s. From Bernard Kops, The Dream of Peter Mann (1960) [combined snippets]:
And from Paul Strathern, Pass by the Sea: A Novel (1968) [combined snippets]:
A similar Google Books search for "look who it isn't" turns up 18 matches, the earliest of which is from a 1973 English translation of Amos Oz, Elsewhere, Perhaps (1985):
Nigel Rees, A Word in Your Shell-like (2004) offers little insight into the phrase beyond a very rough approximation of its date of origin:
Eric Partridge & Paul Beale, A Dictionary of Slang and Unconventional English, eighth edition (1984) adds a bit more detail to an entry that Rees really ought to have credited in his very similar treatment of the phrase:
And further useful detail shows up in Tom Dalzell & Terry Victor, The New Partridge Dictionary of Slang and Unconventional English (2006):
For context, here is a somewhat fuller version of the instance from The Queen's Corporal, which seems to have been a screenplay for Granada Television [combined snippets]:
It thus appears that the expression arose no later than 1959, that it is from the UK, that the milieu where it originated may have been the military (the 1959 example), London street talk (the 1960 example), teenagers (Partridge & Beale), or "church circles" (Partridge & Beale).
Why the negation?
As each of the dictionary authors observes, the negation of the expected "Look who it is" serves to render the expression facetious: whereas "look who it is" can (depending on intonation) suggest pleasant surprise on the speaker's part, "look who it isn't" (taken at face value) indicates disappointment that whoever it is isn't someone else. From this reversal of implication arises the term's facetiousness when the encounter is in fact one that the speaker welcomes.
Do people still say it today?
As for the question of whether "look who it isn't/ain't" has any currency today, I note that among the matches in Google Books search results are ones from 2013, 2013, 2013, 2014, 2014, 2014, 2014, 2014, 2015, 2015, 2015, and 2016. That's a dozen matches from the past three years—so whether people on the (UK) streets still use the phrase or not, novelists writing about them certainly do.