I don't think it is like the example you introduced at all. Gengar is probably already running max S.ATK so it doesn't mean you should change anything. However if you keep Skarmory then you aren't altering evs but instead using Spikes on a different pokemon to help kill pokemon like 252HP/252DEF Hippowdon. Okay so what I am getting at here is with Spikes you can ohko the bulkiest Hippowdon NO MATTER WHAT. Wouldn't you rather have the Spikes so that you always know you can ohko him always?
Why would you alter your EVs to kill pokemon sets that are not run? Its like saying Gengar does not 2HKO Vaporeon [lets just say it does 40%, just a random number] with Thunderbolt to a 252 HP / 252 SpD Calm Vaporeon. Is this a calculation you are going to look at? No, you would and should be doing calculations against the most common/likely set. As I said earlier, are you going to base a Focus Blast on Gengar against a 252 HP / 252 SpD Calm Blissey?
I don't want to argue on somebody else's thread but basically I'm just saying that Skarmory is a pretty good lead for this team because the entry hazards guarantee the kos on defensive pokemon, however unorthodox the evs are. Would you want to be up against 252HP/252DEF Hippowdon and not ko it just because you thought that you wouldn't come up against it?Secondly, would you want to be 2hkoed by Infernape's Close Combat just because you wouldn't make a small tweak to your ev spread.