Flying through interstellar space at a fraction of the speed of light is like sitting still, with hydrogen atoms flying at your front end with high energy. There are a few things that happen to the shell you built the ship out of.
Hydrogen and metals do not get along too well together. As your speed increases, interstellar gas, mostly hydrogen, will cease just being butted aside like a bow shock, but will start entering the shell material. It will work a bit like ion implantation, when an ion gun shoots positively charged ions into a target.
At a ship velocity of 0.01 c, the equivalent beam of protons is coming at about 40 kev, at 0.1 c, at nearly 5 Mev, and at 0.25 c, over 30 Mev. The latter is enough to produce nuclear transmutation. All three will produce damage to the metal or ceramic of the shell structure, by dislodging atoms from their existing structure, making vacancies and interstitials, which are extra atoms in the material structure. These two changes are called point defects, and they can move and collect to create structural weakness and damage. The shell will likely be very cold as well, which may complicate the process.
Some of the protons will only lodge themselves in the shell material, not making any changes to the existing atomic arrangements. This happens at the lower energies, and at the Mev energies of higher speeds, not so much. The protons will lodge in the shell, but only after doing some ricocheting off the other atoms, moving them to new and likely less useful locations. If the shell was surface treated, the protons could also undermine the surface treatment by moving the added atoms. This happens in the outer micrometer of material.
Protons, once embedded in the shell material, can often move around, and sometimes collect in a location to magnify the effect of their being there. A location with multiple protons becomes a site where the strength of the material is significantly weakened, as the protons affect the bonding of the original shell material. This is called hydrogen embrittlement. It does not occur in all metals, and the effects on unique shell materials would have to be determined.
The implantation of hydrogen in some other potential shell materials might lead to different problems. In steels with carbon content, hydrogen tends to combine with the carbon, making methane, which dissociates from the shell material and migrates to form tiny bubbles, undermining the strength of the material. If some sort of resin was used in the shell, it might suffer the same problem, only worse. Ceramics without any carbon would be free of this problem, but might suffer from others. Hydrogen bombardment of ceramics is not a typical experiment, so information on the effects are scarce.
At a speed of 0.01 c, running through the normal interstellar gas density of 0.3 atoms/cc, there will be a deposition of about 3 10^16 atoms/cm2. For a speed of 0.1 c, 3 10^17, and for 0.25 c, 7 10^17. These are enough to cause structural defects to multiply, and possibly long before the end of the first year, the outer layer of the shell will start to fail and probably flake off. At lower speeds, perhaps a micrometer a year would be lost, and at higher speeds, some tens of micrometers. This is nothing to worry about for a trip of 100 years, amounting to a loss of a millimeter at the worst.
As noted in the post on nosecone heating, there are large gas clouds in the galaxy, Bok globules, with a hydrogen density thousands of times more than the average interstellar gas. These range in size from about a half light year to thirty light years, and are gravitationally bound blobs of gas, that may sometime form one or more stars, or may have already formed some. Running through these clouds would make the problems of embrittlement and ion damage much more severe and likely intolerable.
A Bok gobule of five light years in diameter would take five hundred years to cross at 0.01 c, but only 25 years at 0.25 c. However, either of these situations would result in a material loss from the outer surface of the shell of a millimeter or perhaps several. Weakening the outer surface of a material that is only a few millimeters thick might result in failure of the material, but something ten or more millimeters should be able to withstand a single crossing of such a Bok cloud. This adds mass to the shell however. If the vessel in question is only a small probe, a few meters in diameter, the additional weight and mass, plus the resulting propellant mass, is not great, but for a colony ship, it is a lot. A much better solution is simply to never plan a course which penetrates a Bok globule.
Stars are believed to form in Bok globules, and they do not migrate out of them immediately. Hot stars blow them away, but lower temperature stars would still be embedded in one for a period after they begin burning. What matters is the differential speed of the star as compared to the Bok globule. When formed, this speed is likely to be zero. The differential speed would change due to the effect of nearby stars and clouds, and unless the center of mass of the Bok cloud was exactly where the star was, they would begin to pull apart. This process might be of the order of a million years. That means that long before the rubble orbiting the star had time to coalesce into planets, the star would be out of a Bok cloud.
This coalescence time is of the order of ten to a hundred million years, so very likely the globule and the new solar system would be in quite different places. There doesn’t seem to be any reason why an existing alien civilization would want to visit a solar system which was in the process of forming planets. The question is somewhat intriguing however. Would it be possible for the civilization to nudge some early asteroid in the new solar system so it was ejected from the solar system in the direction of their origin solar system? The ejection speed would likely be so slow that a hundred thousand year delivery time might result. It would be a very fanciful scenario to imagine an alien civilization obtaining resources by propelling asteroids from other solar systems toward their own, and then capturing them there.
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