Skill swap is not completely useless if they don't have a magic bouncer. Just set up hazards. That's what Deoxys-S is there for anyway. You miss out on taunt but opponents should try to kill Deoxys quickly because if you are playing HO with a team not weak to hazards then you generally don't care if they set up Stealth Rock against you. It just means two layers of spikes since they elect to not break you sash. Using this Deoxys means you are using Giratina-O on your team. Shadow sneak other Deoxys leads for the 2HKO. Even if you have taunt or magic coat you would put yourself in a situation completely based on luck in mirror lead match up. And that is not a way to win consistently.
I agree that dark pulse is usable but if your opponent has a priority user paired with his magic bouncer then you might get more hazards up with skill swap.
Example with dark pulse: Xatu/Esp gets in and you dark pulse for the 2HKO. E-killer and Giratina-O comes in and takes you out with only SR down. Maybe with proper double switching against Giratina-O, will you be able to get that second layer later.
With skill swap: Magic bouncer comes in, skill swap them and get SR up as they switch to Gira-O or E-killer or whatever to take you out. Should they not switch in their magic bouncer again, you get a layer of spikes as well. It is a bit down to prediction actually, they might try to switch in their magic bouncer again.
Both moves have their merits in a way, but 99% of the time, you will just lay hazards anyway.