Basic relativity: it doesn't matter if you're the spaceship accelerating relativistically through interstellar gas, or you're the scientist on Earth speeding up gas (protons, for instance) in a particle accelerator to research particle physics

Therefore, there's little use in getting bogged down on spacecraft characteristics, or uncertainties on the particle density of the particular area you'd be travelling through to reach your preferred destination -- you can estimate the effects by just looking at relativistic particle-matter interactions and what a suitable dose of those high-energy particles would amount up to.
The xkcd post goes through some of the details of what happens when things pass through other things at very high speeds. You can also learn about it, in a less tongue-on-cheek tone based on actual measurements, searching how any "beam stop" particle physics experiments work. In essence, you electrify (ionize) hydrogen gas to obtain protons, accelerate them through electric and magnetic fields until they are relativistic while you store them in a ring (in a path that has been evacuated to interstellar-space-level vacuum) and at some point let them fling out through centrifugal force to a target. This part is the real-life analogous to relativistic interstellar travel. Usually dose rates will be much higher than what you'd expect in a spaceship, because in these experiments you're looking to produce as many particles as you can, but you can scale by the appropriate amount since the collisions are mostly independent of each other.
Short answer is: all the above answers you mention are correct, depending on the process you're looking at. Cross-sections are probabilistic; that is, there's some probability *any* particle of any size and energy will pass through a given target unimpeded, although this probability will be small for massive, ionizing particles such as alphas or even protons. Gammas and muons will travel farther and possibly scatter while travelling through matter, ionizing things on the way. Electrons will be somewhere in between. You won't worry too much about neutrinos unless passing next to a supernova

Fission is possible when neutrons are encountered, if as you say the material is fissile, otherwise activation will likely occur - although you can have the neutron moderated down in energy, to then be absorbed (with gamma emission), or even reflected, if it encounters the right materials. In general you won't get macroscopic effects such as melting, because there won't be a well-collimated, narrow beam you're travelling through unless you're really unlucky. See the attached picture of T2K's beam target for an extreme case of what long-term proton bombardment looks like on a titanium alloy SSEM (Segmented Secondary Emission Monitor, basically a foil that lets you know how many particles you're outputting through the accelerator beam).
PS: What we call "cosmic rays" are 99% of the times protons, electrons or alphas (helium nuclei)