I use a recipe that calls for removing the top third or more of Cayenne peppers in order to remove most of the seeds. Seems like a waste to me. Aside from having to strain out the seeds after cooking, what would it hurt to just cut the stem and cook the peppers with the seeds in there? Would it have an ill affect on the taste? I wouldn't think so since the seeds are also used for crushed red pepper.
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.
The heat isn't in the seeds, it's in the ribs which hold the seeds. Also, there is no right answer when it comes to wasting time vs wasting food, everybody has a personal preference on whether to use a technique which saves the one or the other.
You can surely remove the seeds and/or ribs any way you like, by cutting away whatever part you like, or cooking everything or straining. The point of a recipe is to prescribe an exact technique, but it doesn't have to be the only valid one.
The seeds don't contain any heat, they're only mildly hot because they're in direct contact with the parts of the chili that contain the capsaicin. See this answer over at Skeptics.SE for more details.
The real problem with the directions in your recipe is that it's suggesting you throw away a whole third of the chili instead of just properly deseeding it! Simply cut it open lengthwise and cut the seeds, pith and ribs away to remove most of the heat.
In regards to the crushed red pepper that you bring up, you can assume that they're in there either as filler or because a majority of consumers still believe that the seeds add most of the heat and would assume that pepper flakes without seeds wouldn't be as hot. As JanDoggen rightly pointed out in the comments, the dried seeds will still add some heat due to their indirect contact with capsaicin but for most cultivars their scoville rating is insignificant compared to the rest of the chili pepper and pales in comparison to the placental tissue which contains the most heat. Details of some values can be found in this related answer
Whether to remove the seeds and ribs from your peppers depends on what you want from the sauce. It's all about balancing chili heat with chili flavor - the more seeds and ribs you remove the less heat you will get without reducing the chili flavor at all, as the chili flavor is all in the flesh. This is your personal choice, there's no right or wrong answer.
Removing the seeds but not the ribs is an option you may want to consider as some chili seeds can be bitter, and having less seeds in the sauce may be better for aesthetics.
It's been a long time since I had seen my mother make her own chilli sause. I had forgotten this step. She would remove the stems and put the rest in a blender. Add some water and blend. Once blended very finely, she would drain it all through a strainer, into a pot. It did not seem that she waisted much in pulp, whole fairly getting rid of the seeds quick and easy.
Agsin, it's been a long time. So, I am hazy of the memory and if that is surely how she did it or my imagination. Though I am pretty sure when I remember stuff, it tends to be spot on.
Best to use a small sample group to try and test, before donating all you, or a bulk of your peppers into this method.
I have tried to deseed the permppers before drying them out more. And, trying to strain them out of the powder, which I used the blender to grind pretty farm Both are a pain in the back.
Though with my mothers method I remember she would have a sause with no seeds. Then would poor it into a large plastic container with a plastic lid. So, whenever she wanted to use the sause, she would pull it out of the freezer, defrost, and the start cooking the sause in a pot to add whatever other spices iused in her sause. Basically salt and pepper. Taisting it from time to time to get the desired taste.
I hope this helps for whoever's may come by and read this forum.
Bets to do an quick and easy experiment with a much smaller sample group.
Oh, keeping the seeds in the sause, which I have done before, just did not seem right. The sause was not as smooth and creamy, but had these hard sees mixed within. It was not the taste it affected but the texture that was off.
So, if the texture of the seeds still being in is no biggy for you, then there is no need to bother reseeding your chilly before hand or when at the sause phase.
I since found a video simular to what my mother did, but not exactly. It was under the search, How do you strain chili sauce?
Watch "How to Make New Mexico Red Chile Sauce from Dried Peppers" on YouTube https://youtu.be/A_8JS7Y4uj4
I think when my mother had them soaking in water, it was in part to get a good bulk of the seeds to wash out of the chilli, after she had removed the stems.
The oil and flour, she did not do. Though when making the sause for others, who usually loved the sause but would say it was too hot, she would ass flower into the sause to cut the heat.
I will add, my own cooking experance, that when I had made some meals too spicy hot to eat, one thing I had tried and seems to help to a degree was add some oil to the sause or soup i,was making. It felt as if the oil would cover whatever was making it taste too hot.
It would make a big difference. If after that, it was too hot, I would some times add cheese. Thinking it is milk that helps counter the heat in chilli. And, or, I would make an vanilla float to drink with whatever I had made too spicy
Si, just adding more experance here.