Are long-tube headers a waste on a bone stock 5.3, or are there real gains over stock manifolds?

Not a waste, but don't expect a transformation. Bolting headers onto an otherwise stock engine won't turn it into a tire-fryer. Speedway's rough generalization is 5 to 20+ hp from aftermarket headers, with the bigger gains on heavily modified engines that move a lot of air. How much you get depends on displacement, compression, cam and tune.

Where headers pay off is as part of a combination — a cam and a tune on a 5.3 take better advantage of the reduced backpressure and scavenging. Headers help two ways: less backpressure (the piston wastes less energy pushing exhaust out) and scavenging (exhaust pulses create low pressure that helps pull the next charge out of the cylinder). Long primaries scavenge best.

Reasons to keep manifolds on a stock 5.3: they're compact, they fit, they need little maintenance, and they sound quieter. On an EFI engine, a tune helps you get the full benefit from headers. Check local emissions rules before removing factory parts.