The ISS does occasionally maneuver to avoid space debris, but not frequently. From a NASA FAQ:
Does the International Space Station have to dodge orbital debris?
The U.S. Space Surveillance Network regularly examines the trajectories of
orbital debris to identify possible close encounters. If another
object is projected to come within a few kilometers of the
International Space Station (ISS), the ISS will normally maneuver away
from the object if the chance of a collision exceeds 1 in 10,000. This
occurs infrequently, about once a year on average.
That's only good for debris large enough to be tracked. Smaller debris is typically mitigated using Whipple shielding, which is basically a thin layer of outer shielding spaced away from the skin of the spacecraft. Anything (small) that hits it at orbital speeds is vaporized on impact and the resulting cloud of plasma disperses somewhat as it traverses the spacing distance, reducing the damage to the spacecraft skin.
Besides maneuvering or shielding, you could also mitigate risk by staging your equipment in an orbit less affected by orbital debris. The height of the ISS was constrained by the reach of the craft that resupply it, but if you're designing to leave Earth orbit altogether you presumably have the ability to send people beyond LEO if the lower orbits are too risky for your taste. Also remember that you're only staying in LEO for preparation, you don't have to manage anywhere near the longevity of the ISS.
Given the options for dealing with orbital debris and the experience we've gained from operating the ISS as long as we have, I'd say that space junk is going to be a consideration when designing and planning manned Mars missions but I doubt it will significantly impact the mission when it's flown.