I'm not going to say any of that isn't true, but speaking as an Icies main I can say that that sort of resource management has its cost. Pikmin don't invalidate grenades or tranqs. They may stop them, but you're considering one side of that situation. The other side is that Snake has a myriad of tools to kill Pikmin. Of course, there's different risk/reward for that (hitting a grenade on the Pikmin is different from hitting a tranq on the Pikmin is different from a Pikmin detonating his d-smash), but that flip side still exists. Like, Nana can also eat tranq with a quick dash dance, but now you've got a sleeping Nana. That example has more immediate consequences, but it still illustrates my point. Olimar has gotta play around his Pikmin carefully against a character with a lot of projectiles that can kill them, because he needs them in order to perform 98% of his moveset. That may be trivial in practice, though, because I don't main Olimar or Snake, so idk.
Now, in terms of a matchup, I can see how Olimar would be disruptive to Snake's gameplan. Plucking more Pikmin would give Snake time to bury more bombs or pull more grenades, so the projectile game would get kinda frustrating after a while. Another thing to consider purely from a zoning standpoint is that Snake does have a crawl, making arcing the Pikmin to hit him a lot more difficult. Also Olimar's game plan revolves primarily around hitting people with Pikmin to build percent, force approaches, and more importantle bait out unsafe moves meant to remove the Pikmin so that Olimar can punish, so when the Pikmin do hit Snake, he's uniquely suited to limit the means Olimar has to approach him while he removes the Pikmin. All that having been said, in a straight CQC fight, I can see Olimar having an advantage just due to his disjoint and good punish game. Snake's hitboxes are in all the wrong places to actually approach people or stop approaches, so he relies on his special moves. Olimar kinda messes with his special moves. It's just unclear how much that actually affects Snake's gameplan, and how much it hurts Olimar in the process.