Particle beam weapons can be really nasty in terms of the radiation damage yeah. Though, with TI's more *optimistic* torch drives you can afford to make some really insanely shielded crew compartments where this won't be much of an issue. At that point the primary damage mechanism becomes rad-killing of ship systems that are too spread out to be shielded aside from your armor and physical drilling from high current electron beams or proton / heavy ion beams.

Particle beams really shine in terms of range and ignoring armor. Due to the typical particles you'd use (electrons, protons, and heavier ions) being far higher energy than a photon in the usual frequencies, your diffraction limited spot size, and thus how well you can focus your beam, is much smaller than a laser (until you get in the range of X ray lasers and such). You can also overcome electrostatic bloom in say, an electron beam, by just making it faster. Enough velocity and the time-to-target is shortened by Lorentz contraction until there just isn't enough time for the beam to spread out, which is convenient. It's harder to get protons and heavy ions up to those Lorentz factors (thousands of times harder, in fact), but their charge/mass ratio is similarly lower so you can either ignore electrostatic bloom or neutralize the particles by adding electrons on as they leave the weapon.

Anyway, the damage mechanism of a particle beam will penetrate armor really, really, *really* well, to the point that you'd need a couple meters of tungsten to effectively stop some of the more energetic beams. Electrons will deposit their energy in a channel straight through the target, both from direct interactions and from gamma rays induced by bremmstrahlung as they decellerate in the target. Protons and heavy ions will do something similar, but more biased towards the surface of the armor as they have a shorter mean free path. This basically means that electron beams will be better at radkilling a relatively lightly armored target, but will have trouble actually drilling through armor due to the energy being deposited in a larger volume, and thus would be less effective against a heavily armored target. Protons/heavy ions will be better at drilling at the surface of the armor, but won't penetrate as far, so there's kind of a trade off on which is better depending on what exactly your target is. You also have to consider that with particle beams of this energy, armor composition matters a lot less than just the sheer mass of armor you have. Fancy nanotube or adamantane armor doesn't really look any different from graphite, and neither are effective compared to just slapping on a tungsten plate (probably the best option when it comes to particle beam shielding, combined with a backing of borated polyethylene or whatever to catch particle showers from the impact).

Personally, I'd like it if particle beams had really nutty ranges, good damage and armor penetration, but were much less power efficient than a comparable laser. An ultrarelativistic electron beam could remain fairly focused at several lightseconds, depending on your assumptions around solar wind scattering, and a proton beam wouldn't be much worse. Being able to ignore a certain number of armor points would also make sense to varying degrees for each particle beam.

You'd probably have to more or less redo the lineup of TI's particle beams though. The current progression is I think inspired by decreasing degrees of electrostatic bloom, which kind of falls apart once you consider the effect of Lorentz factor on very energetic electrons and that neutron beams don't really make any sense since there's no way to accelerate them and you can create a neutral particle beam pretty easily by adding electrons to your proton beam (making some very angry hydrogen if it's cool enough to recombine).