I don't understand how it smells. I have several naturalistic terrariums with cypress mulch or eco earth, fake plants, live plants, climbing structures, and hides. The only things I have ever smelled is the fresh substrate smell.
What are you cleaning with? I use healthy habitat and really like it.
For spot cleaning:
I remove all snake waste and the substrate to the cage bottom. I then spray and clean with healthy habitat. Then I spray with water and wipe it again.