Rabbits are very clean critters. The reason they are so easy to litter train, is because they naturally choose a designated place in their enclosure to go. A shovel, and 5 gallon bucket will make short work of the few piles....great for the garden too! Some of my rabbits are over 5 years old, and have been living on the ground their whole lives, never had parasites ever. The only time I have seen worms in a rabbit was actually fly larvae from a caged rabbit that got diarrhea from too much fresh greens too quick after a winter of pellets.
5 foot by 5 foot is not big enough for a colony, I would want that much space per adult breeder. 20'x20' for 3 does, and a buck would be good to breed, and raise kits to harvest.