Most Hard drives can't fill up SATA 2 anyway, SATA 3 is something for Sold State disks and faster. So for MS it is a way to save a few bucks on each system. When you sell like 5 million, then these bucks start to add up. Take the common 7200RPM HDD (3.5 inch, Xbox one S, and the X probably as well use, 2.5 inch and probably slower than this, source Wikipedia *1), it reads at about 1030Mbits a second, sequentially. That's about 1Gbit a second. Sata 2 supports 3Gbit/s *2, thus you have 2Gbits for your BluRay UHD drive (if you read from both sources at once, which most games won't as nobody will leave the disk in) and everything else that requires the SATA bus.And again, the Xbox One X will use a far slower 2.5 inch drive.
To put it short, Sata 3 is overkill for your standard Spinner HDD especially if you only have one of them like these consoles have. Now if you have a high speed Solid State disk, then suddenly SATA is starting to feel it's limits.
. But since you can't change your disk in the system anyway, it is more than enough.
*1:
https://en.wikipedia.org/wiki/Hard_disk_drive#Data_transfer_rate
*2:
https://en.wikipedia.org/wiki/Serial_ATA#2.0