It has to do with the origins of the words.
All the words that end in -ess came to English with the Norman Invasion from French and Latin. In fact, the suffix -ess is itself derived from French -esse. So words ending in -ess are of French origin. Almost all of them came to be used from Middle English (ME) onwards:
King and queen on the other hand come from Anglo-Saxon.
King and queen
King and queen are both native English words--Anglo-Saxon words:
- king comes from Old English cyning (alt. cyng)
- queen comes from Old English cwēn
cwēn originally meant a wife, specifically that of a king or another important man. Etymonline says that the original sense (i.e. wife) has been specialized by Old English to wife of a king.
Larry Trask suggests that the current meaning of 'queen' is 'improved' because of 'Melioration' (Semantic change). Melioration is an improvement in meaning. He says that queen formerly just meant 'woman', but today it means queen (the female monarch of a kingdom). [Trask's Historical Linguistcs]
In summary, all the -ess words are French/Latinate words while king and queen are native words and don't take these endings.