How do you estimate time elapsed without external inputs? Experiments where people cut themselves from external stimuli seem to show that on the contrary, we don’t good internal clocks on this regard.
I nearly always "know" how long I have been asleep, unless there's been excessive drinking involved (and that would be long ago). "Normal" drinking doesn't seem to affect this. And for shorter naps (less than two hours) it's pretty accurate.
People probably do this based on experience. You know from the wall clock time that you slept, say 7 hours. So on a daily basis, you know what 7 hours of sleep feels like and from that you can extrapolate: if you think you slept about half as much, maybe it was 3 hours. Kind of thing.