Step out of the emotional triangle between you, your niece and the kids' mom. At issue is your attitude/relationship with your niece. Deal with that. Take accountability. It's a minefield for most folks, even worse for young adults.
Family members by marriage can be casualties during a divorce process. Cousins deserve to remain cousins. As my 25 year old niece on my former spouse's side recently told me, "It's always been Uncle Bill and Aunt Kathleen. I couldn't let Uncle Bill take away MY Aunt Kathleen."
So.. this isn't about explaining yourself to the kids' mom because that's not what is at issue. It's about keeping a direct line of communication open with your niece. Cuz anything you say to the kids' mom based on her text puts you on the defensive.
Communication works when it's a straight line, the proverbial straight from the horse's mouth. Otherwise what you get is straight from the horse's other opening.
My advice about the text from your kids' mom. Work with your niece. Address her fears and insecurity because it is scary loving folks enough to walk in the middle of a war zone.
Leave the 'bait' behind. Keep Coach's "Questions are answers and answers are questions." in the back of your mind. And.. is a reply really warranted when actions speak louder than words? At most, "thanks for the head's up. I'm so happy our niece is maintaining contact with the kids."