Boutique-roasted decaf coffee beans often are more expensive. But the logic also doesn't hold: it assumes coffee is being sold at or near the cost of its material inputs, and that's certainly not true. If you have a reasonable built-in margin for your coffee --- and boutique roasters certainly do --- it can be normal and rational to price irrespective of your cost basis. Customers are brand-loyal (especially if they have to go out of their way to buy your stuff). You want to get them in every packaging they're interested in. All sorts of products are "loss leaders", for that reason, and here we're not even talking about that; we're just talking about something slightly less profitable.
Finally, just a note that the "lower-quality bean" thing is itself sort of hollow, in that: you're probably not buying the absolute best quality means no matter what coffee you buy, even if you're driving to a coffee roaster to get them. Unless you're an extreme coffee weirdo, there is, I'd confidently bet, a higher-quality bean available to you that you're sacrificing because of cost and convenience. Certainly, if you're buying beans of any sort at a supermarket, the "best bean" thing is inoperative.
The price difference between cheap supermarket coffee and high-end local roaster is large enough (up to 10x) that the potential additional cost for decaffeination doesn't seem that big of a deal if you're looking for coffee at the higher end of the quality scale.
Not so much? Like I said: decaf beans often are more expensive, and they believe margin hits for decaf are unlikely, which is probably not at all true unless you're talking about Starbucks.
Finally, just a note that the "lower-quality bean" thing is itself sort of hollow, in that: you're probably not buying the absolute best quality means no matter what coffee you buy, even if you're driving to a coffee roaster to get them. Unless you're an extreme coffee weirdo, there is, I'd confidently bet, a higher-quality bean available to you that you're sacrificing because of cost and convenience. Certainly, if you're buying beans of any sort at a supermarket, the "best bean" thing is inoperative.