Since you’re:
Installing a completely new pipe system,
Building a new pool shell 4–5 inches inside the existing one,
And the old eyes (return jets) are located in the outer wall,
Essentially creating a “pool within a pool”,

Here’s the answer:
Yes, you absolutely need to cap or seal the old eyes and plumbing.
Even though the new shell will be inside the old one, the old penetrations (eyes, drains, pipes) in the outer wall can:
Leak water into the old void space between the two shells
Create pressure buildup, water stagnation, or mildew
Eventually compromise the integrity of your new structure if water migrates back or seeps in



