It would make grid based path finding and games so much easier. I know a big part of scratch is the animations, but 480-480 would give even more room for artwork.

(480 is dividable by 32, a multiple of four which is the minimum number of pixels needed to make a square (besides 1, I choose 32 because it allows quicker programming but 360 also dosnt work for 16px squares).

I just don't get why they have one axis dividable by 32/16 but the other isnt?

480x360 is a 4:3 aspect ratio. This shape rectangle is very common, in videos, (older) screens and a few other things. That's probably why it the scratch player follows the same ratio. Plus, it looks way better rectangle, rather than a square for most purposes on scratch.