...it depends on who would own/use them.
If they're purely civilian vessels (to be operated under contract to the military?), then they fall completly outside of the sim rules.
If they're to be "reserve" vessels - i.e. built by/for civilian uses, but with the intent-at-origination for probable later military use - like the Filipino Orca-class whale factories - then I'd suggest budgeting part of their cost under "government furnished equipment" - engines, provision for armament, that sort of thing. (They will, of course, also need a refit later to fit the armament when actually impressed...)
If the ships are to be strictly military owned from keellaying onwards, of course, you pay the price. ;-)