Are lap or slip joints directional.

In "theory " yes. Next pipe down the line should be on outside of previous pipe.
But consider this..
Is there any restriction ( hood, grille etc) for air getting into your air inlet ?
Is there any restriction for air getting to the air filter ?
Is there any restriction for air getting to the carb , throttle body, injectors, etc ?
Is there any restriction for air/ fuel getting into the head ?
Is there any restriction for air/ fuel getting past the intake valve ?
Is there any restriction for the exhaust getting past the exhaust valve?
Is there any restriction in the exhaust gasses getting into the exhaust manifold / headers ?
Are there any tight bends in the rest of the system or reducers going into or out of the mufflers ?
Some of what goes in, has gotta come out. If not, there would be no "exhaust"
Most any welded seam exhaust tubing (except "seamless" ) l have ever dealt with has excess weld inside the entire length which, guess what, is a "restriction "

You MAY have a couple of other things to consider than if a couple of joints ain't exactly " correct ".
You could always grind / bevel / taper the "inside of the inside" pipe to create a smoother flow, l suppose.............
I wouldn't worry too much about a couple " wrong way" joints unless everything else is "perfect ".