it does. I imagined this ship as very versatile. If it flies full armor, the ballisitc missile side port components will simply be replaced by more armoring systems and shield points.
To activate the ballisitic missiles, much armor and shielding area must be removed, this takes lets say a matter of 4 hours in a small shipyard, installation of all the systems plus the missiles, and there you go. However, due to the Coalition lack of err material, these situations will be very rare as ballisitc missiles arent easy to produce, so it's there mainly to scare off people.