Has The Academy ever addressed the issue with acting categories being gender separated?

I don't believe so.

I'm happy to be corrected, but I don't believe this has been addressed. However, this isn't that rare. There are many award shows that distinguish between gender. Talent shows distinguish between male and female singers. Sports differentiate male and female athletes.

So whilst this segregation at first stands out, when we look at other award shows and other categories of entertainment, it's actually quite common.

On top of that, it wouldn't be very beneficial for the Academy to comment on this. Regardless of whether they support it or not, they would have to deal with criticism. Considering the issues they are having right now with #OscarsSoWhite and a lack of diversity in the make-up (and award winners) in the Academy, the on-going segregation of female and male awards is not something they're likely to want to discuss.

Focussing instead on the possible reasons why this segregation continues to exist, I'll quote from Pacific Standard, who did an article on this:

• In the top 500 films produced from 2007 to 2012, only 30.8 percent of speaking roles are filled by women.
• Only 10.7 percent of those films featured a gender-balanced cast (half of the characters being female).
• There are 2.25 working actors for every working actress in Hollywood
today.
• Ninety-one percent of working directors are male.
• Eighty-five percent of working screenwriters are male.
• Eighty-three percent of executive producers are male.
• Ninety-eight percent of cinematographers are male.
• Only 35 women were nominated for Academy Awards in 2013, as opposed to 140 men. There were no women nominated for directing, cinematography, film editing, original screenplays, or original scores.
• Seventy-seven percent of voters in the Academy of Motion Picture Arts and Sciences are male. (Seventy-seven percent!)

And from later in the same article:

Here’s another statistic: Only four women in the 85-year history of the Academy Awards have ever been nominated for Best Director. Lina Wertmüller (Seven Beauties, 1975), Jane Campion (The Piano, 1993), Sofia Coppola (Lost in Translation, 2003), and Kathryn Bigelow (The Hurt Locker, 2008). So far, Bigelow is the only woman to take home the golden statuette.

So if they did merge the male and female awards into a single category, there is a real chance female representation in the awards would dwindle given the demographics of the Academy and the statistics quoted above.

Therefore, the evidence suggests merging the categories (in theory, to end the segregation) would simply propagate an even more male-dominated awards show.

Ultimately, this doesn't really address your question definitively. I don't believe the Academy has ever discussed this, but I hope I've provided some context as to why they wouldn't have discussed this.