Godzfire, are you asking specifically about the music to the Godzilla movies?
With the exception of probably the first two Godzilla movies, the music was most likely recorded on multitrack equipment. So they had the means to mix in stereo. But the actual movie and LP/CD releases would usually use the mono mixes. Maybe they didn't want to go and remix new stereo versions just for the CDs?
Movies have been recorded multitrack for a long time (so they can combine sound effects, music, and dialoge in post production), but would be mixed in to mono.
Here's some cool reading, which is very helpful:
http://www.mtsu.edu/~smpte/forties.html