Snakes a hard to use charicter. Most people try him out but don't have the patients to truly master him so they go witha meta night or samus. And I like your Sheild c4 tactic i might try that.
As for samus don't worry of you bomb gets sent up. Just adjust the tragectory and make it go straigt again. Then when your over samus Just drop it with L. an uncharged samus beam doesn't go as fast as a strait flying nikata so don't worry about getting hit with the second blast. I should mention this is all theory based on how i know snakes missle works and im not at my wii so you should test this out.
Few problems with your post.
1- You're right many people don't have the patience to master Snake, but they don't go to MK or Samus. They go to Ike or Pit. Samus mains/users are starting to drop like flies as a matter of fact cause she is a LOT harder to be good with than both previous Smash incarnations. MK maybe, but out of the swordsmen with the exception of maybe Link, MK is probably the hardest to be good with because aside from his fsmash, he has trouble KO'ing.
2- If I zair a nikita and it gets sent up. Guess what? You won't have time to adjust the trajectory because I'll already have closed the gap, grabbed you, dthrowed and then proceeded to do a 20-40% damage combo while you're in all that lag. Fun fact also, uncharged beam shots knock nikitas off trajectory.
3- Know one thing that kind of throws my zair spam off and forces my timing to be better.
Nade spam. It's pretty annoying sometimes and there's some Snakes I've fought that are pretty good at using it to close the gap, generally with a Snakedash. His jab combo works for being overall pesky too.
If I were to make a list of my hardest to easiest match-ups as Samus. Snake would be somewhere in the middle, leaning towards the easiest side.
My main problem with Snake isn't doing damage to him, that's cake. He is however, a massive annoyance to KO and I dread the thought of trying to KO a Snake regardless of skill level.
Edit: The guy above me posted while I was writing this, he's right on the counters.
Only problem is missile spam has been replaced by zair spam and any Samus who doesn't wait till you're in some kind of lag or some other kind of situation where you generally can't avoid it to blow a charged shot deserves to have it wasted by a nikita.