No she does not know. Emilia only realises Iago's tragic deceit at the end of the play. Earlier, after Othello had accused Desdemona of being a whore, she tells Emilia of her grief at being so accused, and asks Emilia to:
Lay on my bed my wedding sheets: remember;
And call thy husband hither.
When Iago enters and Desdemona tells him of Othello's accusations, he acts surprised and feigns ignorance. He expresses his disgust at Othello's malicious accusation. We learn, at this point, that Emilia is completely in the dark about her husband's manipulation, for she says:
The Moor's abused by some most villainous knave,
Some base notorious knave, some scurvy fellow.
O heaven, that such companions thou'ldst unfold,
And put in every honest hand a whip
To lash the rascals naked through the world
Even from the east to the west!
What she says is patently ironic. She mentions, in Iago's presence, that the person who has informed Othello about his wife's supposed infidelity is an evildoer who is abusing Othello. She goes as far as saying that persons who tell such pernicious lies should have their bare bodies whipped by honest persons from one side of the world to the other. She does not realise that the person responsible for this perfidy is standing right next to her. Iago, obviously anxious that her rant would draw attention, asks her to quiet down.
Emilia is clearly upset and mentions that such a rapscallion as the one she mentioned above, at some point also accused her of having an affair with Othello. These lines make it obvious that Emilia has no idea that Iago planted this malignant suspicion in Othello's mind.
It is only after Othello had murdered Desdemona, that Emilia learns the truth about her husband's complicity. She is in utter shock and disbelief when Othello informs her, as illustrated in the following dramatic discourse:
OTHELLOCassio did top her; ask thy husband else.
O, I were damn'd beneath all depth in hell,
But that I did proceed upon just grounds
To this extremity. Thy husband knew it all.
EMILIAThat she was false to wedlock?
OTHELLOAy, with Cassio. Nay, had she been true,
If heaven would make me such another world
Of one entire and Perfect chrysolite,
I'd not have sold her for it.
OTHELLOAy, 'twas he that told me first:
An honest man he is, and hates the slime
That sticks on filthy deeds.
OTHELLOWhat needs this iteration, woman? I say thy husband.
EMILIAO mistress, villany hath made mocks with love,
My husband say that she was false!
I say thy husband: dost understand the word?
My friend, thy husband, honest, honest Iago.
EMILIAIf he say so, may his pernicious soul
Rot half a grain a day! he lies to the heart:
She was too fond of her most filthy bargain.