No, lance hits dos not pass through shields. A lance hit on a ship with shields will knock one shield down and generate a blast marker.
since blast markers are placed as they are generated does that mean that if one ship fires its lances and generates a blast marker on a target will its batteries suffer the negative effects of shooting through a blast marker?.
Yes, that's correct. The lesson here is: Fire batteries first to knock down shields. Lance fire is unaffected by blast markers