Most of the points made by some responding are true. Creators can only do so much, map judges do their best to catch anything that's left, and anything else is human error. Maps are designed to be done a certain way and we try our best to keep it that way, anything that makes a major difference should be patched.
Now there is a difference between little stuff like cutting a corner and major skips that cut off big chunks of the map or entire checkpoints. The difference is that the small stuff still follows the intended route but larger skips that are multiple blocks or entire checkpoints either utilize a wall/barrier that can be bypassed or straying from the marked route which creates an unfair playing field. (Due to it being secret, hidden by the discovering player, and unaccounted for by staff)
And last thing to address is what gets you in trouble. 1 basic principle, never abuse a skip or even use the skip without consulting a staff member if you don't want to risk getting in trouble. Repeatedly doing a skip for your own benefit instead of once or twice for testing purposes is abuse and may get you banned.
TLDR; Optimizing the main route is okay, skipping a considerable portion of the route is not okay, and always consult a staff member first unless you want to risk an abuse punishment.