It is doubtful whether the humans had to clean the cages every morning. Possibly they had sloped floors or slatted cages, where the manure could fall away from the animals and be flushed away (plenty of water around) or destroyed by vermicomposting which would also provide earthworms as a food source. Very deep bedding can sometimes last for a year without needing a change. Absorbent material (e.g. sawdust, softwood wood shavings and especially peat moss) would reduce the moisture content and hence the odor.
From Creation Ex Nihilo 19(2):16-19,
March-May 1997
™ Version 4.2