It's not recommended to change bedding unless it's soiled or if it's required for disease protocols (ex: ringworm, coccidia) where the animal has been diagnosed and is being treated. You're correct that changing bedding daily increases stress and is not best practice.
The ASV Guidelines for Standards of Care in Animal Shelters has recommendations for spot cleaning instead of full sanitization (including references) in section 5.3.2 Spot cleaning primary enclosures.
This study mentions spot cleaning being less stressful, resulting in less illness and reduced shedding of pathogens: Shelter housing for cats: Principles of design for health, welfare and rehoming
Hope that helps!
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Alicia Naundorf
RVT - Behaviour Interest
Edmonton Humane Society
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