There are two Deoxys's. One that went to Sinnoh and the one that attacked Rayquaza whose fate is currently unknown, drifting endlessly in space. So not really the last time we saw Deoxys, both of them. I have this feeling the writer has been planning some big answers for Sird and Deoxys dedicated to an arc in Sinnoh to be honest. Honestly, now that Cyrus is good and all, I wouldn't mind if Sird suddenly becomes the De Facto Galactic Leader embodying Cyrus's nihilistic and sociopathic views. Now that I think about it, she still does have that mind control machine to create her own mindless puppet army doesn't she?
Deoxys only went to Sinnoh so it could find the meteorite that would allow it to change forms at will. Since it never stated Sinnoh by name (we can only assume it was Sinnoh since it was the only region with a meteorite at the time of that volume's release), Kusaka could easily use any of the available ones.
Also, it specifically stated its goal was to find the other Deoxys, so what reason does it have to not show up? ORAS is three years after the events of FRLG, so it could've gone and taken a meteorite and left on its merry way awhile ago.
In fact it also includes Fiore region.
Oh right, the "third?" Deoxys. That's another can of worms, isn't it? Well, that's what we get for making an unrelated side manga that later turned out to be canon to Pokespe.
Makes me wonder how Darkrai fits into the Shadows of Almia story, too.