I believe David is saying that the handrail bolts go into a steel (iron) threaded plate that is embedded in the fiberglass deck. No bolts are involved. Amel used this technique in many ares, like the engine room hatch cover hinges and pneumatic piston mounts, the bases of many of the stancions, etc.
The problem is that if there is water ingress, the rust you see may be from the embedded iron starting to deteriorate and "bloom". That will eventually cause the fiberglass to expand with the surface bulging out or even opening up - I recall Bebe Bill and others had this issue with the engine room hatch cover at the piston mounts. I had it with a stern stancion actually cracking the cap rail structure open;
So, preventive/corrective maintenance would be to remove the bolts, passivate the rusting internal plate, and "permanently" seal the bolts on reinstallation. Depending on the degree of deterioration of the backing plate you may want to remove and replace it, although you'll have a challenging fiberglass repair job. Alternatively, one can drill out the rusted plate a good distance around the bolt hole, fill will epoxy (like JB Weld) and retap the threads.
Having said that, you may just have some minor surface rust coming from the stainless hand rail base, that is of little concern and easily cleaned up.
Cheer, Craig, SN68 Sangaris