She [Riza] and Roy are both perfectly aware of each other’s feelings, and it’s heavily implied that anyone who knows them well considers them to be a couple.
Confirmed by the third art book. She [Riza] and Roy have known each other since they were teenagers at least - he was her father’s alchemy apprentice - and Arakawa’s comments verify that the only reason they aren’t married by the end of the series is the anti-fraternization law. The Chroniclesbook further confirms that they remain together for the rest of their lives. x