There are many ways to indentify a hologram from a real player:
If a hologram takes damage, it will flicker.
A hologram has no shadow, no secondary weapon, no Armor Ability on its back, and no Gamertag above its head.
In Halo: Reach, a hologram will blink in the Sniper Rifle's night vision screen, the Spartan Laser's small viewscreen, the Focus Rifle's vertical viewscreen, the Revenant's driver-side monitor, and the Gauss and Rocket Warthogs' targeting screens.
In Halo: Reach, Holograms sometimes expose themselves by flickering on their own. This was removed in Halo 4.