Bungalows next to the harbour are resonably clean and not expensive. The hotel next to the fort was being renovated in 2007 and ought to open some time soon. Note: as in 2008, this is not open yet. Otherwise, ask around in town and someone will probably know someone, who can arrange accommodation.
Alternatively, take a car back to Canchungo or Bissau and spend the night there, there are better hotels and restaurants in Canchungo than Cacheu.