NES-era games also ran on bare metal. Modern consoles run proper modern operating systems with everything you'd expect to find in one — preemptive multitasking, virtual memory, hardware abstractions, kernel- and user-mode with syscalls, etc. PlayStation OS is a Unix system (something-BSD IIRC), Xbox's is obviously based on Windows NT, and Switch runs something Nintendo built from scratch.
Cycle-counting doesn't make much sense for code running in a preemptive-multitasking OS because no matter how much you count cycles, the actual execution time for a piece of code would be non-deterministic. That, and I suppose most modern games are bottlenecked by the GPU, not the CPU.
fwiw, the switch actually uses cooperative multitasking. This causes emulation headaches of its own, because sometimes retail games are buggy, but due to the relative determinism of scheduling nobody ever noticed (e.g. race conditions that are reliably won on real hardware will suddenly start breaking in emulation).
Cycle-counting doesn't make much sense for code running in a preemptive-multitasking OS because no matter how much you count cycles, the actual execution time for a piece of code would be non-deterministic. That, and I suppose most modern games are bottlenecked by the GPU, not the CPU.