You can probably use some feet or material to make sure vibrations don't cause the top sub to shift off the bottom one, and I would assume the existing feet are sufficient to deal with most of the vibrations.
The downside is really the loss of smoothing out the bass response due to having both subs in one location, as kr4 mentioned.
The downside is really the loss of smoothing out the bass response due to having both subs in one location, as kr4 mentioned.