It could become strained. Naruto snapping at Kakashi would create an initial rift between them. Kakashi might be taken aback by Naruto's outburst and Naruto, after snapping, might feel a bit guilty but also stubborn about his feelings, which would make the relationship tense for a while.
Well, their relationship might take a turn towards more honesty. After Naruto snaps, they might have to sit down and talk about what's really bothering Naruto. This could lead to a deeper understanding between them. For instance, if Naruto snaps because of Kakashi's training methods, they could discuss and find a better way that suits Naruto's learning style, which would actually strengthen their bond in the long run.