Also, be vary wary of Snake's C4s and Claymores. They both take 30 seconds to disappear (the C4 will explode while the Claymore does nothing). A Claymore can be detonated with a dash->perfect shield or a D-Smash.
Claymores disappear upon death. C4s stay on the field. When Claymores time out, they disappear. When C4s time out, they explode. I cannot remember the exact timing, but my gut is telling me that the C4 is on a 42 second timer, or something to that extent. 30 seconds is too short for it.
Despite what people think, I honestly feel that Snake does average on Rainbow Cruise. Snake only has issues when the stage is climbing, and when it moves to the right before it has the solid platforms. If a Snake actually -camps- and plays smart during the ascension of the level, and rides a carpet up. [Attack him, and you WILL be shield grabbed vs a good Snake into a Down throw, which will result in obscene damage since you will have no where to roll. He can then shield camp with a grenade until you approach, or spam Mortar's until you get the 'timing' to approach to bait you into it.
Furthermore, Snake will be able to take advantage of the relatively small size of the Ship. F-Tilt, Up Tilt, Mortar, and C4 almost take up the entire length of the ship. The entire later half of the level with the walk offs prevent any gimping of the Cypher. Let's not forget the relatively low ceiling in the second area.
Needless to say, if you take a Snake to Rainbow Cruise that is aware of the layout of the level, who plays smart, you aren't going to win that as a counter pick.
I honestly believe the same can be said about the other counter picks you list. Jungle Japes always leans to the player with the better projectile. Snake has grenades, and thus can grenade camp one of the platforms. When ZSS approaches, he can perfect shield the ->B approach due to the predictability. If ZSS approaches the actual platform he's on, he'll be able to shield grab to Down throw, which SHOULD result in large sums of damage. The main weakness on this stage is the fact that Snake likes to kill up with Up Tilt.
Other tidbits...
-You say to Dair the Mortar, but the resulting lag will leave you open to a tilt, another Mortar, a grab, etc. You're better off Air dodging, or utilizing down B to change your momentum.
-I don't really see much mention of grabbing. When fighting Snake, it's extremely risky for ZSS to grab him. There's so much lag in the move, that if baited into a Grab, Snake can just spot dodge into an -easy- Forward Smash, grab, Tilt, or otherwise nastiness. In regards to grabbing, the best thing ZSS can do is Down Smash to Grab to U air, U air, etc vs Snake. Due to his heavy wait, this work exceptionally well.
-The first stock is the most important one for ZSS. She needs to rack up damage with the Suit pieces. I'm sure this is true with most match ups, but more so with Snake. When you have those three pieces, you're going to be able to pressure Snake, extremely well. Unfortunately, you don't want Snake to get those pieces. Snakes are used to throwing things, just remember that. One of my favorite things to do against a ZSS is to grab one Piece and throw it up, in tandem with a Mortar. It makes a rather potent wall. The ZSS will then rush to pick up the piece, usually resulting in a Dash attack, which leads to a Shield grab, or worse.
Just my two cents, but then again I don't win tournaments. =p