In 1.1 I found them fairly easy to navigate, pass them on their corner and they don't multiply. If there is a real need to go through one I found melee better especially if it inflicts hugely excessive damage. Otherwise leave them alone.
I haven't done enough spelunking yet in 1.20 to know if they're more frequent. In the previous version, puffer frequency seemed ok to me. Even on levels with them, it was usually possible to avoid them entirely, or enough that they weren't usually much of a problem.