Karai's mother is in her mini briefly, but it seems like she doesn't talk to either of her parents at this point.
Saki and Krang's mothers aren't explored at all, and I think that's a shame. While it
could be argued that maybe Utrom biology allowed Quanin to give birth to Krang, I personally don't think so. And there would still need to be a second parent involved anyway, because someone's alleles beat the living daylights out of Quanin's by most depictions.
Given the time period, I wouldn't be surprised if Saki's mother died in childbirth, as utterly cliche as it is.
Spoiler:
Personally, I would have had Shredder's mother as a kind of "Lady MacBeth"...or a witch who was in on Kitsune's plans. And encouraged Saki to kill his father. Complete with the ollll' Palpatine "Do it".
As for Krang's mother, by IDW limits, I blame her for him being a spoiled brat in his Villains mini. Maybe Krang would hang out with her once in a while, mostly to wine&whine. His relationship with her would stable enough that he wasn't itching for her to come out of stasis - should she have survived Utrominion's collapse. Which I think is possible.
(I also think she'd be like Scarlett O'Hara if she cannibalized Rhett Butler's pampering tendencies down to a faint ghost of what it once was)
They could be included in their son's stories without changing a lot. Or, potentially, making things better. Just because they're mothers it doesn't mean that they're the force that might stop whatever scheming they're up to. Heck, they could encourage it, or maybe just not care all that much.
I even think Casey's story could be a touch more interesting if his parents might have been divorced, and somehow Hun managed to twist the law around his little finger to get full custody just to stick it to his ex. As such, Casey has no idea where she is and smacked into the light bulb that would make him figure out how to find her. Maybe even Angel could be from a divorced family.
Sure, divorce is just as tired a trope, but I would much prefer that over the mother being dead. We don't need half the cast to be a herd of Bambis.
The turtles, as far as I'm concerned, are the only characters where it would make sense for their mothers to be dead. And Saki's. Because it's been 200 years. It's more in regards to story significance. Casey's mother doesn't NEED to be dead, nor does Angel's. There could always be divorce, being too much of a druggie/alcoholic to notice or care about her child being abused, or just hanging around in the background but still being at least a little present.