There is a sort of penalty, but not very severe:
By sinking ships inside your patrol area, or succeeding secondary missions you get points to distribute at the bunker afterwards for improving your sub and crew performance. Everytime you put the crew in 'Battle Stations level 2' they act according to their performance which can be seen if you fire-up the crew window and click on a crew image to see his details. You need to manually distribute a crewman's points (until you read 0 points), don't forget that, especially for sonar man, or they act sub-optimal.
If you skip your orders and patrol elsewhere, then you won't get these crew points or points for your sub, that's it I think.
Also in SH5 there is the quirk that once you enter your patrol zone, you should not leave it early because the time counter to decide if you are successful will be reset if you save the game inside the zone. To avoid that, stay in your zone in 1 go and only save once you leave the zone. Not patrolling the ordered time will also 'only' get you as a penalty no points for your sub and crew. (sorry for my English, this makes it a long text...)
The sticky post for TWoS is a long one, but it's worth to read because it contains many finesses about the game and how you play TWoS, so I recommend to read it.
Cheers,
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