The only think that fits under the seat on my '09 is a small tool pouch... Did the earlier M-series have a shovel recess... ??
To be honest, unless you're riding in flatland where there is no avy danger, I really believe that your shovel should be part of your backpack.
If your buddy gets caught in an avalanche, you want to be able to ride to where you last saw him/her, hop off your sled, and HAVE your shovel, probe, and beacon readily accessible. My shovel rides very nicely in the outer mesh of my KLIM backpack. Before that, I had a cheapo walmart pack that also had an outer mesh/web part and the shovel rode there.
If you do have an under-seat storage area, it's likely there was an arctic cat branded shovel that fit it. It would be a good place to stash a spare shovel, since it is possible to break a shovel in hard avalanche snow...