Snake-Eyes' profile in the game states that he prefers his Jitsu powers, and his Katana sword. This means that he does not use the ammo that the Joe's use -- therefore he has unlimited ammo. Also, other than Gen. Hawk, he is the best jumper in the game.
Hint: Jumping stats
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Quickly press A, B x2, Up x2, Down, Select at the title screen. The sound of a gun will confirm correct code entry.
Use Grid Iron or Rock 'n Roll, jump over the holes in the floor, and attack Cobra Commander in the face. Change control to General Hawk when low on energy, then fly to the top of the screen and attack.