Bodies such as Enceladus, Mercury, and Triton, etc... have thin (and often temporary) atmospheres.
When probes or landers encounter the chemicals in such atmospheres in low orbits/landings, they may find themselves experiencing adverse chemical reactions that could potentially jeopardize the mission.
My question is: How/(do they at all) aerospace engineers account for these factors?
I'm assuming you mean reacting with the probe itself?
We know the atmospheric composition of these bodies.
The examples you listed:
Mercury, from NASA:
Instead of an atmosphere, Mercury possesses a thin exosphere made up of atoms blasted off the surface by the solar wind and striking meteoroids. Mercury's exosphere is composed mostly of oxygen, sodium, hydrogen, helium, and potassium.
Enceladus, from Wikipedia (also backed by other sources):
91% water vapor 4% nitrogen
3.2% carbon dioxide
1.7% methane
Triton, from NASA:
Triton's thin atmosphere is composed mainly of nitrogen with small amounts of methane.
According to some people on Quora and this site, The Apollo LEM was made of Aluminium (Aluminum) and a little bit of steel. While alumnium is quite reactive, it quickly forms an unreactive layer with the oxygen in our atmosphere, stopping it from reacting. Obviously this isn't a great example because the LEM didn't go in an atmosphere. According to NASA, the Persaverance rovers were also made of aluminium and titanium, so the point stands.
So, I guess they just work out what the atmospheric composition is, and build spacecraft out of relatively unreactive elements. Obviously things like RTGs will have unstable elements, but they are protected by inert materials.
Hopefully this helped?
While Earth's atmosphere isn't thin near the ground, it's certainly thin higher up in LEO where spacecraft can orbit.
At some altitudes within this "thin" part of Earth's atmosphere there is a lot of atomic oxygen: O instead of O2 (UV light from the Sun dissociates O2 and when these atoms re-thermalize they have higher velocity for the same kinetic energy per particle so the monatomic oxygen ends up at higher altitude than O2 or N2. Even lighter He and H dominate even higher up for the same reason.
Monatomic oxygen is highly reactive and eats metal and especially organics like plastics and rubber. Spacecraft that fly in low LEO are definitely (usually!) carefully designed so that exposed surfaces can withstand atomic oxygen for the duration of the mission and the monatomic oxygen can't easily get inside the spacecraft where it can wreak havoc with all kinds of things.
For more, see the following questions and their answers:
Source: https://commons.wikimedia.org/wiki/File:Msis_atmospheric_composition_by_height.svg
