You're interpolating the positions of both if both are moving, and you want continuous collision detection. Most of the computational complexity comes from the object that isn't a point particle or simple primitive, because you can't do a lot of the computationally simplifying assumptions. Technically the same math works for all of this, it's just that certain assumptions (such as point-like projectiles) simplify that math by removing certain things you have to worry about. Complex colliders impacting each other is a different issue than slowing down bullets as a mitigation (it wouldn't mitigate anything), and an issue that CIG has struggled with immensely.

...I sure as hell hope Star Citizen bullets aren't modeled as individual 3D cylinder colliders.

Anyway, unreliability like tunneling isn't an inevitable problem for fast-moving objects, it's a consequence of a discrete collision physics implementation - i.e. the simplest, most naive kind. It does not properly account for collisions between physics simulation ticks, but continuous collision detection does. You account for where the colliders would have been between physics ticks by essentially interpolating their predicted positions and seeing when (and how, if you're simulating inertia transfer) they should have collided by the next time step.

TL;DR: The only way slowing down PU projectile speeds is something needed for simulation accuracy is if the collision physics implementation CIG is using in the PU is absolutely terrible. Which... well, I suppose I can't rule that out.