This is something I've struggled with for awhile now, and applies to both transcription and composition.
So, let's say we have a song at 160 BPM. The main subdivision is eighth notes, and the beat (quarter notes) is clearly emphasized by drums (so it's a fitting written tempo). However, for every chorus of this song, the pulse halves - although you could certainly still tap out the beat at the same speed, it "feels" like the song has slowed. Assuming the written tempo is still 160 BPM, the main subdivision is still eighth notes.
So my question is, should I change the written tempo to reflect the hypermeter? In this example, it would mean halving the tempo to 80 BPM, and the eighth note subdivisions would become sixteenth notes, even though they are technically identical in speed and duration. Would that make it more readable?
I should also mention that in this example after the chorus, the hypermeter speeds right back up, slows down again in the chorus, and stays slowed for the rest of the song.