I believe there is sufficient evidence to support that neural implants are an optional “upgrade” (optional to all except perhaps the ship captains) in Halo. In the Data Pads scattered across Reach, we see two things:
1- AIs require them to enter the human mind
2- AIs had a form of government known as “the Assembly” (which is irrelevant, aside from potentially playing into Halo 5/6’s story)
Second point of evidence is the lack of scarring on marines in Halos 2, 3, and potentially 4 and Reach (which I haven’t checked).
The third point is Forward Unto Dawn- when Lasky tricked the enemy team he had his team take off their helmets, not their skulls.
The fourth point is Gabriel Thorne- when he was teleported onto Requiem by the Forerunner box thing, they couldn’t find him. If he had neural implants, or any other kind of implant, they would’ve been able to find him instantly.
Now, rolling around to point one again, some of the helmets don’t have a slot for an AI, which, once again, does need the implants to enter a persons’ mind. All suits of Mjoinir (butchered that spelling) are capable of supporting an AI, many, even, wanted to have an AI for each Spartan to turn them into unstoppable killing machines. This idea was scrapped due to expense.
Here on Waypoint we learned that AIs are being built into every suit of Mjolnir to help with ammo count, radar, and so on. With all this knowledge combined, I believe it is possible that the neural interface simply does not exist in Spartans who choose, while the majority do take them. My guess is these AIs would be used to make up for the lack of NIs.
It is also notable that a surgery is required to remove the implants, which are so tricky to remove there is a high chance of death. This again sounds impractical for use by the UNSC.
But that’s just a theory… A game theory!
Edit- a month later and I still found another few points to add in my favor- one is thanks to Dr. Halsey below.
The first new point is Glasslands-
Jackals prefer the UNSC with neural interfaces in their skulls over anything else. This implies not all UNSC have the implants.
The second new point is rounding back to Halo 4. The IFF tags you gather all around. They are dog tags with recording and tracking equipment in them. This would be a clear alternative to NIs for troops who opt out. Most marines don’t have the scar on their head from it, as seen in all Halo games with marines.
“Options are optional”- Sarge
Third point is in Halo 3-
Cortana picked up a friendly contact, but who would be crazy enough to come in here? Arbiter. He didn’t have implants, but was detected. Dog tag IFF is a good explanation. Same for the other friendly Elites in game.
There was also the missing marine and Spartan teams you find who would be suddenly detected by Miller once you got close to them. Switchback. Dog tag IFFs might not give a very good signal compared to NIs, but are less dangerous so would be more widely used. This is my evidence.
Edit 2-
One could argue “signal jammers”, but fire team Crimson was still perfectly detectable.
Anvil Station is a canon location where SoS Elites and Spartans are training together in a Warzone Simulator. Elites wouldn’t dare let anyone chip them, as it is seen as losing honor to lose blood outside of battle.