Or ships on the same team have shields at the same ‘frequency’ (or whatever) which means they can pass through eachother, but they are still impervious to the enemy.
This would facilitate additional gameplay like there could be some way of obtaining the enemy shield frequency, eg. Staying super close to a capital for a period of time to scan the shield fluctuations. This would be difficult as you’d be a prime target, but if successful you’d be able to pass through enemy shields for some time, eg 30 seconds, until they changed the frequency, and inflict a load of damage.
Edit: This would also mean a friendly ship couldn’t dock if it’s shields were down. In such emergencies maybe it would be necessary for the carrier to momentarily drop its shields, adding to the peril and drama of the situation!