Actual literary analysis is so rare around here that I feel compelled to respond to this.
The reason it's only one parent per child is twofold. One, having both parents be in conflict triples the amount of time I need to spend dealing with it, because you need to examine the father-child, mother-child, and father-mother relationships instead of just one parent-child relationship. This is further compounded for every sibling that appears in the story. Family issues already take up a fair amount of space, so anything I could do to streamline them is a good idea. And two, the main characters ultimately turned out OK. Thus, they needed to have at least one stable loving parent in order to not be total basketcases. (Haley, whose stable parent died early, is also the most screwed-up, psychologically.) Therefore, the first parent who was given definition in the story became the one that would be more prominent, and thus the one that caused conflict. Which leads us to...
Then Elan finds out his dad is an evil warlord in #50, but even then, it was intended simply to explain the differences between Nale and Elan. I suppose I could have made Elan's father the happy-go-lucky waiter and his mother the warlord, but that didn't feel right. Not so much because of Elan, but because of Nale. Nale has the sort of damaged ego that would force him to try to surpass his father at all costs, which of course would fail and thus lead to his presence in the dungeon. If Nale had been raise by an evil mother, I think he would have been more of a "corrupt prince" sort of character rather than an angry rebel looking for a magic doodad to go back and seize power. In this case, plot dictated characterization.
I didn't get the idea that Tarquin would ever appear on camera until much later, when we saw Haley's ransom note in #131. At that point, it needed to be Haley's father that was imprisoned simply because if it were anyone else in her family, her thief father would be the one trying to save them instead. In fact, that was the case for all three sets of parents: if both were active and present, then it would have been their spouse dealing with their issues rather than the child. Since it's the child's story, the spouse must be absent or otherwise incapable of acting.
All other examples are apophenia. Redcloak's parents are irrelevant to the story; his father could have been a saint for all we know, but he wasn't killed by the Sapphire Guard. Kubota and Therkla had a teacher/student relationship; she was raised by her loving parents. Shojo did not raise Hinjo from childhood, so the relationship was never truly parental. I guess a case could be made for Miko, but I see that as more of a "bad child" situation than a bad father one. Miko was Miko long before Shojo started lying to her; his ruse started only a few years ago but Miko was 28 when he said that.
So, I'm afraid that any connection is simply an emergent property of the fact that I started the comic without any sort of plan for where it would go. That doesn't mean that you can't analyze it if you want though, if you're a "Death of the Author" sort of critic. Just please don't speculate on my family life in the process.