If it was a big squishy poop at risk of an overflow blowout I would.

If the nappy can't handle another round of pee or poop then yeah I might consider waking the baby up to avoid them waking up thanks to the pee.

The secret is in changes before naps though :)

You might be underestimating just how deeply children sleep.

My kid gets her diaper changed several times a night and sleeps through it. If she does wake up she cries for a drink of water then immediately goes back to sleep.