Rob,
If I were to read into your first statement, you seem to be implying that the Cubans would have stockpiled seeds from all the strains they have used in the past. This makes perfect sense! I suspect that the Estación Experimental del Tabaco de San Juan y Martínez would be where these legacy seeds are stored.
Now as to the different strains and their characteristics in fermentation, I haven't a clue. But again, what you say does make sense. I wish we had a tobacco expert here who could speak to this. Like you, I also wonder what the Estación might have missed when Sancti Spiritus 96 was commercialized. Do you have any further information on the years of cultivation of that strain and the vintages it might have ended up in? Would 1998 have been the first?
One final point. From a marketing/commercial perspective, reviving the older strains might not meet with wide acceptance with the vast majority of smokers of Habanos who have taken up the hobby in the last decade or two. On the one hand, it's a matter of what you've grown up with and what you have "learned" cigars should taste like. My experience with pre-1980's Habanos is almost nil but they do taste very different from what you can buy today. Perhaps not better, but certainly different.
On the other hand, I could not see Habanos reverting their existing marcas back to these legacy tobaccos. I could more readily imagine a case where they would release Limited or Special issues using these ancient strains and targeting the "connoisseur" of the "old Havana taste."
Wilkey