Indeed, in Action Stations, it is said that the only way to penetrate the capship shields in use at the time was through saturation bombardment--you needed either the plasma cannons on other capships, or else an entire squadron of fighters all shooting it at once.
Shields and weapons seem to go through cycles in Wing Commander. At the start of each cycle, capship shields are nearly impenetrable except through overwhelming force. Then a weapon capable of penetrating capship shields--usually a torpedo--is developed--it takes a number of seconds to lock on, so only heavily armored craft such as bombers carry them. Later on, advances in computers make it possible to shorten the time needed to decipher the enemy's shield patterns so that ordinary missiles and guns can penetrate. This creates an incentive to develop better shields, which starts the whole cycle over again.
We witness two full cycles of this in the WC stories--in Action Stations, shields reign supreme, but in WC1, all fighter weapons can penetrate shields. In WC2, it has gone back to having only specialized weapons being able to attack capships, but by WC3, even the Arrow can take down a Fralthi once more. In WCP, the pendulum has swung back towards shields, and again only torpedoes and heavy guns can damage capships.