I'm an intermediate hobbyist with no external obligations to play. I get canker sores a couple times a year, and while I could probably still play without pain sometimes (depending on where they are) I usually take a break for the two weeks or so while it heals.
I don't really have a rationale why. I don't think sax necessarily causes extra bacteria/trauma/change in oral hygiene. I just take it extra easy on my mouth during these times (now is one of them).
Do you take a break or do you play through it?