Are they always present or is there such a thing as a disease free hive? :?
No such thing as a disease free hive if you mean that none of the pathogens or pests are there. But that depends on your definition of "disease". It's normal for a hive to have a lot of "pathogens" living there to some degree. Most all have Varroa mites. Most have Tracheal mites. The fungi that cause chalkbrood and stonebrood often live in hives without causing undue problems and actually the fungus that causes chalkbrood prevents EHB.
http://www.bushfarms.com/beespests.htm
Just like people. No matter how healthy you are or how well you feel, you are not disease free. You always have the rhino virus. (common cold) and a whole mess of others.