Sometimes they slip up, and I think it was Skype that ran into problems where some releases of OSX shipped a faulty or missing 32bit driver for some particular iSight/FacetimeCam models.
(on the other hand, as you say, it might be more difficult to run a multi processor setup sharing RAM and buses across completely incompatible ISAs.)
You know, Universal binaries that contained both PowerPC and Intel within a single fat binary...
Double size binaries is nothing compared to the amount of storage you have today.
On OSX: combinations of PPC, x86, x86_64 could be built
On iOS: default at the moment is a triple of armv7, armv7s, arm64, I believe. For a while used to be armv6+armv7.