Thomas and his wife and daughter were residing in or near the Boletarian Palace when the Demon scourge arrived. Thomas went mad with terror and abandoned his wife and daughter rather than fight to protect them. When he regained his senses, he found himself in the Nexus being cared for by the Maiden in Black. His wife is of unknown age, but Thomas describes his daughter as being about the same age as the Maiden in Black, if she were still alive. Since the Maiden in Black has the outward appearance of late teens / early twenties and Stockpile Thomas describes his daughter as "young," it is possible quite a deal of time as passed between the Boletarian Palace falling and the player arriving in the Nexus.
The player finds two corpses suspended by chains from the side of a tower. On one corpse is a jade hair ornament, which identifies it as Thomas's daughter, and the other wears raggedy robes and carries Fresh Spice. Since they are chained next to each other, it is assumed the second corpse is the wife of Thomas. Fresh spice is sweet smelling so it is possible she carried it as a type of perfume. But, since the family was likely not royalty, she probably had the spice for its use to regain MP, further implicating her as a magician.
It is unknown why the demons singled out Thomas's family to be hung as most corpses are just left on the ground. Perhaps it is because they are woman as most of the Demons and corpses left on the ground are men. Yuria also received special "attention," locked away in a tower by herself and violated by the Fat Ministers. It is possible Thomas's wife and daughter suffered those same indignities before they died.