They fly through resource asteroids all the time, in normal Sins. Suns, too, for that matter!
What's worse is that every Advent trade ship flys straight through the starbase when it docks. It seriously ruins the ambiance.
Ship pathfinding is one thing I really wish they'd fix, in general.
Watching ships in Homeworld used to be like watching ballet. It was epic. Sins ships, however, bounce off of each other, fly through each other, clump up, and accelerate/decelerate in jumpy little spurts, and I hate to say it, look kind of bad.
One thing that I think could actually be fixed rather easily, with the fighters, is that I really wish they'd deviate from the ecliptic plane, sometimes. They should swoop in and out of a battle, over and under, but mostly they fly along on the plane, clipping with everything, all clumping up into one ship, and making these zero-roll turns. Not to compare red apples to green apples, again, but Homeworld fighters swooped around doing loops, and it was awesome.