First, a clarification must be made about radar. Radar, like light photons, is NOT reflected. Rather, the energy is absorbed by the object, and then retransmitted. Materials that conduct electricity are far better at retransmitting the radar signal than are materials that do not conduct. Fiberglass DOES sent out a very poor radar signature, compared to a metal hull. Stealth aircraft are, in part, made stealth by coating them with substances that do not re-transmit the radar signal, but rather absorb it. The energy is dissipated in some other form, usually heat. See Radiation-absorbent material
If you provide a very thick layer of radar-absorbing material between the exterior and any machinery, the radar image would be severely degraded. Even if the radar signal reached the machinery, it would still have to get back out. Turns out, some foams are a really good RAM.
And, of course, since you do not need any interior crew compartments or crew spaces, you can fill the entire superstructure with foam.
Dissipating the heat is made much easier, since the boat is riding on a very large heat sink. The ocean would quickly dissipate the heat, with proper cooling fins.
Now, back to your boat. Several answers allude to structural integrity. Foam-filled fiberglass does have a lot of structural integrity. The stresses are spread throughout the entire volume of the foam, so although on a cross-sectional basis, foam is a poor structural member, when the entire volume is filled with foam, the member becomes highly structural. That is the basis of packing large screen televisions in solid foam. The stresses are distributed throughout the box, not just along structural members.
Laminated foam and fiberglass sheets are an even stronger structural member. That is, when spraying the foam, embed fiberglass sheets and rods into the body of the foam, not just the envelope.
It is not unknown for larger fiberglass boats to have a steel frame, bonded to the fiberglass and embedded in it, to add critical reinforcement.
I would suggest using a common ship-building technique - a strong keel. If the keel is made of metal, below the water line, this would go a long way to giving you the structural integrity you need. A keel that forms a typical truss beam down the center of the boat, even better. Think open web trusses. Maybe two or three cross trusses midships.
Since radar is usually from the side, not from above, then using flat steel trusses in the horizontal decking, especially if just below the waterline, would keep the radar image to a minimum.
I would suggest making it all electric, using solar power and batteries, to eliminate any heat signature from combustion gases. Again, the heat generated could be dissipated in the water, not the air.
Reinforcing the foam with steel structural trusses, and embedded fiberglass sheets and rods, would give you the structural rigidity you need. With no need for any crew spaces, the entire body can become a solid structural member. Electrical engines would reduce the heat imprint, and placing as much weight below the waterline would give good stability. Since there are no crew members, sea sickness is not an issue, so let'r'rock'n'roll.