Say you are in a happy future where mother ships travel between Earth and the Moon, or Mars, or Venus on regular runs, and are met by shuttles at each end of their voyages that transfer people, cargo, and fuel to the ships, after which they continue on their way, looping back and forth. (As I understand it, if you can invest in the necessary infrastructure, this is the best way to do it. If not, another question is necessary.)
Would repeated aerobraking maneuvers when entering orbit add up to significant stress on the ship over time? If fuel was no longer a major concern (for instance because it is now produced off-world and is cheap and plentiful), would it be better to avoid such aerobraking in order to extend the life of the ship?