I have another take: market.
Efficient use of those 9-axis accelerometers, that do little more than giving the 9 values with various filtering options, is inherently difficult (AHRS algorithms) and requires frequent recalibration (especially the magnetometer), which is not ultra-convenient neither for engineers nor for end-users.
IMUs embedding AHRS algorithms directly are starting to appear, and I'm betting that they'll be replacing the more "raw" 9-axis IMUs with no signficant internal processing.
The 6-axis ones are still useful for more basic uses, such as approximate device orientation. On mobile devices, which I'm sure are the biggest market share for those MEMS IMUs these days, the magnetometer is rarely more than a gadget than can be done without for simple orientation purposes, and is mostly used for implementing compasses, which is not all that useful for most people. And since they are rarely used to really implement accurate AHRS, they don't need to be placed inside the same package.