Milos Columbo kills Aristotle Kristatos, James Bond throws the ATAC off a cliff in front of General Anatol Gogol, and the film closes on the yacht with a parrot taking calls from MI6 and the Prime Minister. It sets up no direct sequel.
Why does Bond throw the ATAC off the cliff? Because the device is useless to Britain if the Soviets can also claim it, and Bond refuses to hand it over. In my opinion, it is the most practical choice in the film, since the whole plot has been a tug of war over one object and the only way to end the tug of war is to remove the rope.
The moment before it matters as much. Bond stops Melina from killing the surrendered Kristatos, which respects her need for revenge but denies it a cold blooded execution. Kristatos then pulls a hidden knife, and Columbo's thrown knife kills him, so the villain dies with a weapon in his hand and nobody has to carry the moral cost. I think that is a tidy piece of plotting, and a neat contrast with the earlier scene where Melina kills Gonzales with a crossbow.
The final yacht scene is a light button on a film that spends most of its runtime on cliffs, wrecks and snow. Melina's parrot, which earlier gave away the meeting phrase that led them to the monastery, now fields the calls from MI6 and the Prime Minister, so the one animal that cracked the case also gets the last laugh.
Seen against the rest of the series, the ending stands on its own. For Your Eyes Only is the 12th official film, arriving after Moonraker and before Octopussy, and because it sets up no direct sequel, nothing in the yacht scene points toward Octopussy. In my opinion that makes it a closed story: the ATAC is destroyed, Kristatos is dead, and neither Moonraker before it nor Octopussy after it is left a loose object to pick up. It also sits eleven films after Dr. No, the first entry, in a run of 25 official EON films, and its answer to the question of who keeps the dangerous device is to let nobody keep it.