Here's a little thought experiment for you:
The International Building Code makes a table for estimating costs for new construction (actually it's to calculate an appropriate building permit/plans review fee to cover costs associated with new development, but that's irrelevant to what I'm positing for you).
ANYWAY.... the chart lists cost per SQUARE FOOT based on the occupancy use (Assembly, Business, Factory, Hazardous, Residential, Etc) and building type (non-combustible/protected steel; unprotected non-combustible; ordinary (concrete/masonry); heavy timber; wood frame) - this is extremely simplified... I know nothing about ship construction (or how to relate the IBC to it), but this is an okay place to start.
I suggest the following:
1) Upgrade to square meters (let's be simple, so multiply by 10 and call it even)
2) Use Type I, H4 (the ship carries hazardous cargo in a hazardous environment.... ) - but you could use any of the sets for something (R3 for repair/modification of a stateroom, Assembly type for the bar/crew lounge etc... whatever fits logically into what you are doing (consider the ship a multi-use occupancy... but for ease of use H4 is what I use).
3) Add the standard Naval Architect Fees to draw up the plans, apply for the permit, have the plans reviewed and approved, and any necessary inspections before completion/final approval of the project... anywhere from 1 - 10%
REMEMBER: the shipfitters union at the shipyard won't work on your vessel without approved, permitted plans... shipboard (starport/military) inspectors will also examine any and all work done to maintain space worthiness, etc - and of course your remodelling plans and permit become a permanent part of the ship (for future spot inspections) - what do you think the military looks at when doing a board and inspect op?
Oh, and don't forget... your next stop in port to repair battle damage? Any concealed spaces (DM to find?), field repairs, installations, or modifications can be inspected and evaluated for code compliance (and perhaps a correction notice and fine to require upgrades?)
You don't need to use the bureaucracy part of this suggestion, but it can be used for additional flavor/realism/adventure/etc.
What do you think?