My guess is this issue could be due to sounder file configuration.
Since v 1.5, new .lua files were added into the sound directory, located in the sounders sub-folder. Sounders files for naval vessel weapon systems can be found in your DCS World's sound folder in > Sounders/GroundUnits/WeaponSystem/Navy.
There are lua files of the ships respective of their GT.Name. Copying and renaming a sounder lua file to the GT.Name of your ship mod will do, but considering the weapons are different, the sounder code in the .lua file will have to be altered.