Actually, they're not. However, their shields are immune to its effects, neutralizing them right at the beginning.
NSAU Fighters enjoy the same level of protection, allowing them to hold their own against anti-fighter units such as the Bacteria (canister) turret and the fearsome Liquidator.
Do note though - the shields will still take basic projectile damage.
NSAU ship hull however, are not immune to such effects and will suffer the same hull devouring damage like UNC ships do.
Therefore if a NSAU ship shields are down, a single projectile carrying the bacteria can infect the ship even after shields are being regenerated. The infestation carries on from within; shields deflect only from the outside.
There's another caveat though. Bacteria infestation do not finish off starships and structures (leaving 1 hp). They do with fighters though. Therefore, if your NSAU ships are badly infected; beat a retreat and your ships might still survive.
Have fun!