I'm not sure about the "most programs" bit. I think you're forgetting whole swathes of programs like system utilities, databases, tools etc.

But, in any case, this is why we build large programs using modular architectures. You don't profile the Linux kernel hoping to find a hotspot in some obscure driver somewhere, you profile the driver directly. Same for filesystems, networking etc. Similarly we build libraries for things like arithmetic and SAT solvers etc. that will be used everywhere and optimise them directly.

Your comment reads like you're disagreeing with your parent, but in fact you are reinforcing the point. We've forgotten how to build programs like this and end up with big balls of mud that can't be profiled properly.

I completely disagree. If the program doesn't have "hotspots" then it's probably pretty fast and it's following Knuth's advice. But in my experience most applications are completely littered with "hotspots" - endpoints taking 5+ seconds to respond, reports taking minutes or hours to generate, stuff like that. I've never worked on an application where I didn't quickly find multiple easily avoidable hotspots. The average developer, at least in my area of the world, just really doesn't understand how to write performant code at all. They write algorithms with terrible time and/or space complexity, they write inefficient database queries, design their database schemas in ways that don't even allow efficient queries etc.

Then they add caching to compensate for their crappy system design and stuff like that, bloating the system with lots of unnecessary code. They store the data naively then spend significant processing time preparing the data for delivery rather than just storing the data in an ideal format in the first place. Lots of stuff like that.