There's not much point in optimizing something if it's only called once. Likewise, you may have something that's very fast but called a million times, so it could be worth trying to make it even faster.

Of course, if you can take some item and Benchmark two solutions for it and pick the faster one, that will be better for performance in all cases. However, the time you spend doing that might have been better spent working on something else. That's what profiling will tell you—where your program actually spends its time in a real run.

If you're writing a module, you can't always tell how it will be used. Otherwise, test your program to see where it really spends its time, and optimize those places where it will make the biggest difference. There's no reason to guess about it if you can test it easily.

As for your concern about approximations and calls within calls, the profiling tools can give you meaningful statistics either way. You can look at time spent only in a certain function or in the full cumulative time spent in that function and everything it calls.