1- Did those houses really came with character files (is it even possible when the lot was shown as empty on the exchange)
2- If character files cannot come with empty exchange lots, could these 2 characters files created by the game when I edited my downtown and Univeristy lot?
3- Is it bad that I deleted them.
If the house was empty, then it contains no character files. If it had been a family, it would have been put in your occupied lot bin and you would have 2 extra sims running around. The game frequently creates new character files, for NPC's and townies, so that's what you probably deleted. You should never delete a character file without knowing what it is. So in answer to your question, yes it's bad that you deleted them without knowing what they were. However depending on what character it was, you might be able to get away with it.