I HATE stuff like that and I'm sure that I'm worse than most about obsessing over these little things! I've been known to cut a stab out and redo it because it was off just a hair. Just today I tore down the modded front deck on my 4 Star 120 build and redid it because I didn't like the lines. That's the neat thing about building and Scratch building......you can make it however you want.

Now, to your Q, no, it won't make any weird stuff happen in the air. If it's going to bug you from now on, redo it!