Should I get waterproof or breathable mesh shoe bags?

It depends on what you pack. Waterproof or water-resistant bags (like drawstring PE pouches or coated nylon) are better for muddy, wet, or post-workout shoes because they contain moisture and dirt. Breathable mesh or quick-drying fabric bags are better for clean, dry shoes you want to keep aired out, since sealing damp shoes can trap odor.