I've always found that other considerations (desired antenna height, field of view, mast structure weight limits, allowance for crane motion, limiting radhaz to crew, keeping rigging away from rotating antennas, etc) limit antenna placement so much that you just live with the fact that you simply have less than the ideal amount of real estate to play with. For example, at times I have had no other choice but to mount a GPS receive antenna within inches of a VHF whip, and VHF/UHF whips within a few feet of marine radars, and found no ill effects. At other times I have found RF interference problems due to emitters that were not even on the ship.
Unless you are involved in a major military project you're probably better off with a few rules of thumb (and perhaps some extra bandpass filters) than the cost and effort of developping an accurate RF model of the ship.
The most common naval technique of reducing radar cross section is to limit/eliminate corner reflectors within the ship's structure. Good examples are the Canadian CPF and French Lafayette designs. A great example is the Swedish Visby Class corvette. The Visby is also an example of enclosing all antennas within a single radome to reduce radar cross section. Another passive technique is applying RAM to high signature areas.
