You’re right that in the Super Powers Companion it is possible to have a character that deals 6d6 damage using at 12 point Attack, Ranged (and this is only possible with Four Color Heroes or higher because Street Fighters have a Power Limit of 10). This does make the character very powerful and able to wipe out most enemies in one blow.
The counter for this is to use better tactics. Unlike other systems like D&D/Pathfinder, you don't make stronger bosses with a bajillion hit points, you make enemies that utilize smarter tactics that exploit this character's weaknesses. Such tactics include:
- Send many enemies: The hero can only attack one enemy at a time. If a bunch of enemies are sent against him, he will be able to knock out one or two with ease before he gets overwhelmed. If he invests in the Area of Effect or Cone modifiers, then the swarm of enemies ought to be staying in close proximity to allies since he would hit friend and foe alike.
- Have enemies hide: Enemies can take cover, crouch, hide in darkness, and so on to make it more difficult to be hit.
- Send in armored enemies: Unless the hero has invested a bunch into the Armor Piercing modifier, he is still limited by highly armored foes, especially those in armored vehicles. If you really want to be insidious, you could throw in enemies wearing Heavy Armor, which he won’t be able to damage at all unless he takes the Heavy Weapon modifier. If the enemies aren’t fully encased in armor, then he’ll have to take Called Shot penalties to bypass the armor which makes it even more difficult to deal his damage
- Make it a priority to Shake the hero: This might be done with Tests of Will, Tricks, or just hitting first. After all, if the hero is Shaken, he can’t deal damage and will have to roll a high Spirit or spend a Benny. It’s possible that by investing in so many powers, the hero has a bit of a glass cannon and if he gets Shaken or Wounded, he’ll be unable to hit anyone.
- Focus on taking him out first: Related to the last one, being such a powerhouse means that enemies ought to concentrate on eliminating this hero before going after the others who will presumably be easier to take down.
- Get into melee and stay there: If the hero's trappings are a rifle or larger, then he’s not going to be able to fire in melee at all. If his trappings are a pistol or smaller, ranged attacks in melee are possible, but go against the enemy’s Parry, rather than the standard TN of 4. This will mean he is going to have a more difficult time hitting enemies in close quarters. Enemies could also try to grapple him, giving him a –4 penalty to Shooting unless he gets out.
So there are lots of ways to limit the effectiveness of a 6d6 attack without resorting to power negation or anything like that. Again, the key is fighting smarter. “Bosses” will know of this character’s abilities, meaning that they ought to plan their confrontations around that and make sure he won't get a clear shot off at them.
However, another option might be to just tell the player that you will have a hard time challenging such a specialized character. In Savage Worlds, Rules as Written™ is not nearly as important as having a character everyone at the table is happy with. For instance, you can create characters with a Charisma of +8 or even +10, but GMs should probably tell players that they won’t be able to challenge them if they try it. I personally wouldn’t go so far as to outright ban 6d6 damage super heroes especially if I can use the tactics above, but rather I'd just suggest to the player that both of us would have more fun if the character became less specialized.