You can't miss it because it doesn't even come close to running along the grain line in the spruce top. A structural crack will virtually always follow the grain along the weaker light grain line between two hard, dark ridges of grain.
Finish has no grain structure, so it can crack in any direction. Finish cracks or "checks" may follow the grain in a "general" way, because the wood may have expanded or shrunk across the grain and strained the finish. Usually, though, such finish cracks will stray away from following the grain exactly. Sometimes a structural crack will proceed for a while, and at its end a finish crack will continue. This pattern can get a bit confusing.
So far we've looked at the thin sections only. If you see several cracks at the heel of the neck, or behind the nut where the peghead might be broken, chances are you're looking at finish cracks.
Here's a really gross example:
These cracks are obviously in the finish, even though they follow the grain of the neck and side. Structural cracks don't generally occur in multiples, and never like this!
This one is obvious, too:
The heel is cracked, and the same crack appears to continue along the sides, emanating from both sides of the neck. There's only one crack, so we can be reasonably certain.
The crack continues to the body, so we can be sure that the crack goes right through the neck block and looks just like this inside:
This is a big structural crack that must be repaired for the instrument to survive.
Three top cracks in this 1887 Martin guitar extend from the bridge all the way to the end of the body:
They are structural cracks, but will not affect the longevity of the guitar even if they are left wide open and not repaired at all. Spruce has very little strength across the grain, and the pull of the strings is never in that direction. So, lengthwise cracks have little effect on strength in this area, where the only force is with the grain. The wide bridge (now off the guitar) distributes the load across six inches of the spruce, so it's able to handle the tension very well.