The last scene of them in the anime shows them engaged in a friendly duel of kendo, with Nanami serving tea. This scene holds clues to the ending in several ways:

First of all, Saionji and Touga are duelling, but it is a practice fight with no real intent to harm behind it. Before whenever they duelled, the duels were violent and out of control. But with the passing of the revolution, all that is done with. The duel here is a healing duel, to show that duelling can be used for good (here: to cement a friendship) as well as for evil.

Nanami's serving tea to both Saionji and Touga shows her letting go of her posessiveness towards her brother. By serving both of them tea, she's willing to share her brother with others and to find joy in it at the same time.

Saionji says he's taking more classes to make up for the time he spent "playing around." This makes it obvious that both of them remember something, but nothing substantial. Perhaps in the future when Akio's influence on their memories wears off, they will remember, but for all they know now, they have spent a normal few years at Ohtori studying and engaging in normal high school intrigue.

Also notice that there is no hint of the sexual interplay between Touga and Saionji as there were in the previous few episodes. All the more to suspect that the sexual tension was a product of Akio's meddling as well. Now that his influence is gone, Saionji and Touga are simply friends...and perhaps it's better that they don't remember that they were anything else.