Drivers would be the only justification. If they really cared about 16-bit apps they would have supported them on 64-bit Windows: it's only real mode and virtual 8086 mode that are hard to support on a 64-bit OS; 64-bit compatibility mode can handle 16-bit protected mode software just as easily as 32-bit software. Additionally, virtualization works fine for application-level code, but not drivers.
After 32-bit Windows Server went away as of 2008 R2, I didn't expect MS to keep shipping 32-bit client for this long. Anybody have a convincing argument as to why? 16-bit legacy apps in large businesses?
Obviously it's not free to do this, especially since they'll be producing every patch for two PC platforms for probably another decade.