Mission planners were worried about the pilot and commander losing flying proficiency and/or being affected by extended free fall on long missions.
Flight rule rationale section:
Crosswind limits for EDO flights and night landings include a somewhat
arbitrary reduction to 12 knots peak to allow for additional piloting
margin due to uncertainties in pilot performance degradation from
increased exposure to zero-g and reduced depth perception,
Space Shuttle Flight Rules page 2-22
(EDO stands for Extended Duration Orbiter and refers to a suite of Orbiter modifications and add-ons which allowed extra long missions)
Note that this rule was never invoked for mission duration; the longest shuttle mission was STS-80 at 17 days, 15 hours, 53 minutes, which included two days of weather wave-offs.