They had already planned their trilane from the start, that's why Naga. The issue is they should actually have changed it when they saw Nyx pick. You can't go Mirana trilane against Nyx cause he just stands in front of your arrows and carapace and you're fucked everytime you try to kill someone, and if you sleep Nyx then other support transfers and Nyx still carapace the arrow(no cast point on it). Overall though top lane wasn't too much of an issue, it wasn't going well, but Alch wasn't farming well either. They were winning mid and winning bot by a lot since Furion left the lane a couple of times and loses to Weaver anyway. What they didn't take into account was the early teamfight potential with meka+ravage, Orange just 5man pushed all the towers and then well, it's hard to do shit because you're 6-10k gold behind even if you don't give up kills.
I think Na'Vi drafted the better lanes and more or less won early game, but they drafted an awful teamfight setup against what Orange had(mirana arrow into birds/carapace, bane ult against birds/ravage, weaver against concoction+soulassumption) so they lost as soon as Orange stopped laning.