One of the most maddeningly frustrating things is when you have a flight that will fill to capacity one way but the return flight is either completely empty or nearly so. Usually the cause is connecting flights going one way but not having the corresponding connecting flights going the opposite way. Finding the problem when you are small isn't difficult. Finding it when you have 100, 200, or more planes in operation gets a lot harder.
On a new airline I'll cancel/move this type of flight. On an established airline I may continue to fly it even though it ends up being a (small) loss.
If both flights contain a lot of passengers with internal connecting flights from or to them then removing them would also cause a negative effect on those routes as well unless those seats can be filled with other passengers. So if it's not completely asymmetrical but more like 100%/60% then keeping it would be the better choice, even for smaller airlines.
At the end of the day just an observation and a grumble. No big deal really. On established airlines I'll usually keep this kind of flight. On a new airline in a competitive market I'll shut it down and try again later once I've added more flights elsewhere hoping I've fixed my connection issue.
I would really not put to much interest into this particular route. When you run a big airline it is indeed hard if not impossible to micro manage it. I for example have 7 large airlines on 2 different game worlds which is hard to actually manage especially as I am not working with running my fictional airlines full time. I came into the same issue earlier so I totally reset the account and decided to only run 1 holding but later I added one and then another and all of them have their own subsidiaries.