Hot sauce; Remove seeds?
I just made a batch of hot sauce that was very cayenne-heavy myself. Keep the seeds. 

You want to get every last bit of heat out of those babies, especially if you are diluting with a significant amount of vinegar. 

The only use case I can think of for chopping the tops off as described in your recipe is if you aren't already planning to strain out the pulp as well. 

Even if I was eager to keep pulp but avoid seeds in my final batch I would rather scrape seeds from the individual peppers than waste that much product.

I personally don't think you'll notice any off flavors from the seeds.