The last lines of the story reveal that Armand did not know of his black ancestry.
"But above all," she wrote, "night and day, I thank the good God for having so arranged our lives that our dear Armand will never know that his mother, who adores him, belongs to the race that is cursed with the brand of slavery." (Chopin)
A very prejudiced man, Armand does not know that he is the one who bears black ancestry from his own mother. He would behave differently looking at his baby if he knew the origins of the black features were from his side of the family.
Actually, the quote from Armand's mother does not establish that Armand knew nothing about his ethnic heritage before the end of the story (and reading the letter from his mother). Armand's mother, Madame Aubigny, died in Paris, France when Armand was only eight.
What the quote from the letter establishes is that Armand's mother, before she died and before Armand was more than eight years old, believed that her eight year old son was not aware of his ethnic heritage. She could have been mistaken and the boy could have already guessed at as much. Even if this is unlikely, it is quite possible he would have learned this from either his father or by reading this letter in the preceding years.
Notice how Chopin does not explain that the letter surprised him or that he read it for the first time at the end of the story (this likely shows that Chopin herself wanted this to remain an open question—especially since the story is even more interesting without a conclusive answer).
As for him behaving differently when examining the child, this would only be true if Armand cared for truth and other people above protecting his own reputation and patriarchal authority. Actually, if he knew about his ethnic heritage before meeting Desire, she may have been a convenient scapegoat for him from the beginning.
He needed an heir, but could he really risk revealing his true ancestry in this time and place? Her "obscure origins" made it possible for him to place the blame on her from the beginning, thus preserving himself from the scandal.
La Blanche is also an interesting piece of this puzzle if you really want to delve into the mystery of this.
While the story never offers a definitive answer to the question asked here, the ambiguity works to deepen the mystery of the story and reveal the possible depths of Armand's self-hatred and desire to hold onto his slave owning authority.
This is truly a majestic and intricate story, worthy of several readings!
Yes Armand knows he is black. That is why he picked a girl of unknown origin. Then if the baby showed his mothers race he could then do exactly what he did.