For the broken glass and similar bits: so long as it's historically appropriate and physically plausible, it should be fine. That said, it will be best if you make and group these elements such that they can easily be replaced if needed. E.g. don't merge the boarding into other hull wood meshes, keep the windows and nails their own mesh and not merged into metal hull fittings, etc. Does that make sense?
Meanwhile, the approved gun count for the Bahamūt was made after careful and thorough consideration of the ship's construction, its r? and its history. We're already kissing the historic limit of number of guns per deck, especially in light of the fact this is intended to be a refit of a captured merchantman. She's not heavily constructed two-decked warship, but a refitted cargo hauler. While you are welcome to consider other ship plans which might fulfill your hopes, more than 44 guns cannot reasonably be added to this particular ship.