Congratulations on your sd's upcoming marriage! I totally get your and dh's being upset about the seating arrangements, but young people, today, often do things differently. SD may just be doing what she thinks is youthful, modern, and fun.
Sure, maybe it's because of her mother. Maybe she doesn't want her at the Top Table, but is afraid she'll hurt her feelings by having you and dh there. Or maybe she would have had you all there, but was concerned it would be a tense situation. If any of this is so, it just shows you raised a kind, caring young woman who thinks things through.
Whatever, I would try to let it go. I doubt that either you or dh would want the day ruined over who sits where. Please just enjoy the fact that she's getting married to someone she loves and, hopefully, will make her very happy.