I personally don't see anything wrong with them not inviting your dd to the school party, it's more the way it's been done. If your friend had said, look we're just doing a small gathering with school friends, we don't want your dd to feel left out, as up til now we've invited them both to each other's parties since they were little - but now they're getting older, the way we do things start to change for various reasons... If it was me and it was the first time we were doing things differently, I'd be aware of you and your dd potentially feeling miffed / left out and would mention the reasons it's different this year. If she's given you dates to arrange something for them to do together, and then just doesn't bother to actually make any plans, then yes that would be hurtful, but hopefully she will still organise something.
When my daughter was this age she went from being friends with everyone in her class and being invited to all the parties (but also having one special best friend at school) to the classes being mixed up in year 3 and then the girls formed much smaller groups, a group of 4 in her case. She also drifted away from her previous one special bf as they matured, things became less intense, and instead she became one of my dd's group of 3 bf's. They start to have more autonomy and your friend's dd may just want it to be her school friend at her party, there is probably a particular group of them that are close. Your dd might feel left out, or if like you say your girls are so close like sisters, then maybe the mum is worried they'll stay together the whole time and it would effect the school friends group dynamics? There could be so many reasons. If you want to know why, I would just ask your friend. Plus if your dd has her birthday coming up soon as well, you could use that to start a conversation about things, discussing potential plans with your friend and then casually mention you're not sure whether to do separate things this year now that they're getting older, one with dd's school friendship group, and one with said close friend. She's bound to then explain why she did the same.
We've always done separate things with the kids cousins, we tried a couple of parties when they were younger where they came along to the school friends party we were doing, but it didn't work. Either the kids would stay with their cousins and school friends would feel left out, or they'd stick with the school friends, and the cousins would feel left out. If you say the girls are like family to each other, then this may be what your friend is worried about and the reason for the separate events.
Saying that, if your friend put potential dates out there with you to arrange for the girls to do something together, and then you hear nothing else about it, I'd be miffed. I'd wait and see though, organising the school party has probably been the first priority as it involves getting more people together on one date and with more children there it's more to organise. So she may have just not got round to arranging things with you yet? No harm in you asking her if she still wants to do something for your girls on the dates she mentioned?