Why is eMMC in a BGA package, despite only using a small number of pins?
The size of the eMMC package is limited by the size of the silicon chip inside the package. Its size can't be reduced (with current available technology).

The number of pins could be reduced, yes, but it would also make it mechanically weaker, because the package would still be fairly large. There needs to be enough pins to keep the package mechanically connected to the PCB.