This is little more than idle curiosity - I can come up with one good reason, and some additional reasons on my own. I've downloaded, and partially configured Whonix, and the workstation is busy downloading the browser bundle now. Everything looks good so far.
Best reason I can think for using i686 is, you only needed to build the virtual machines once, and they work for everyone.
Other reasons might include, if all Whonix machines use the same architecture and kernel, then it is harder for an outside attacker to distinguish between them.
Or, the guy who built the VM's didn't have a 64 bit machine with which to build them.
Or, it's possible that there is just no 64-bit Whonix? I just looked at the download page again, and it appears that everything is 32-bit.
As I said, it's little more than idle curiosity - but please fill me in!