I haven’t had the time to have a full look through the books to find any reference to those rubies. However, the first mention of them from Ned’s POV is very telling.
They had come together at the ford of the Trident while the battle crashed around them, Robert with his warhammer and his great antlered helm, the Targaryen prince armored all in black. On his breastplate was the three-headed dragon of his House, wrought all in rubies that flashed like fire in the sunlight. The waters of the Trident ran red around the hooves of their destriers as they circled and clashed, again and again, until at last a crushing blow from Robert's hammer stove in the dragon and the chest beneath it. When Ned had finally come on the scene, Rhaegar lay dead in the stream, while men of both armies scrabbled in the swirling waters for rubies knocked free of his armor.
A Game of Thrones, Eddard I
Firstly, it mentions lots of people trying to get their hands on one so the rubies are likely spread around Westeros having been used to make the owners rich. It also mentions the rubies were knocked free of the armour and Ned could still see it was Rhaegar. If most of the rubies had come off it would be likely any glamour would have failed.
Maester Yandel also makes mention of similar events in The World of Ice and Fire.
The battle screamed about Lord Robert and Prince Rhaegar both, and by the will of the gods, or by chance—or perhaps by design—they met amidst the shallows of the ford. The two knights fought valiantly upon their destriers, according to all accounts. For despite his crimes, Prince Rhaegar was no coward. Lord Robert was wounded by the dragon prince in the combat, yet in the end, Baratheon's ferocious strength and his thirst to avenge the shame brought upon his stolen betrothed proved the greater. His warhammer found its mark, and Robert drove the spike through Rhaegar's chest, scattering the costly rubies that blazed upon the prince's breastplate.
Some men on both sides stopped fighting at once, leaping instead into the river to recover the precious stones. And a general rout quickly began as the royalists started fleeing the field.
The World of Ice and Fire, The Fall of the Dragons: Robert’s Rebellion
This related Q/A also mentions that Rhaegar was cremated. It is, however, from a semi canon source so might not necessarily prove your theory wrong.
Lastly, it is worth pointing out that the story is ultimately about Jon and Dany. Having Rhaegar still alive kind of diminishes that. It would also further complicate things with regards to Aegon.