The answer to scout spam is your own scout spam.
Yep, it's that simple. You see, then you BOTH of you will have absolutely worthless fleets.
Ok, now that I have your attention. I believe everyone knows that Raging Amish is the guy that first had the idea to spam scouts and use to attack. HE ALSO DIDN'T KEEP SPAMMING THEM AFTER HE HAD LABS FOR BETTER UNITS. If you have the labs, and have done the research, for the love of all that is sacred, please, please, give me a challenge and spam a better unit. Carriers, flak, or LRFs, they're all good.
I just got done playing a game where the guy had about 10 disciples and 15 illums. I don't know why, but he switched to scouts...SCOUTS!!! If you can already make illums, for pete sake, make illums.
Scouts are good against one thing...LRFs (and structures every 10 min if you're TEC). Do not make tons of scouts 45min into the game unless all you have to your name is a roid and a frigate factory. If you have any labs at all, build a ship that can fight against more than one thing.
This is the way Amish intended it: spam scouts early, then upgrade to better ships. I think 99% of scout spammers are missing the second part.
That it all.
EDIT: This is not a post to tell everyone that scouts are OP, or blah blah blah. This post is to get people to do it smarter.