its done like in any other space sim (as i can remember)
almost all the spacesims have capitalships with shields and almost none of em have modelled shields
shields are simulated with a different hit effect: when shield goes to 0 the hit effect changes in to a hull hit effect
older games had not noticebale differences between the two effects or none at all, in the most recent difference may be more significant
for example in xvt the differences between the graphic effects are very minimal but it changes the sound,
in xwa the energy of the laser hit seems disperding in a minimal area, and when shields are at 0 the effect reproduce instead bruises and holes on hull
in wc prophecy as far as i can remember there is no big difference like in starlancer
and i can't remember in tachyon to be honest
in my opinion even enabling the shields when shield model is not present without changing the effect(so you just can't damage hull until shield is at zero) would be better than now, disabling the standard hit effect when shields are active even better, applying the shield effect or a new one to the hull to represent shields hitted the best possible:)