There are many uses for so-called "flicker" effects like from Essence Flux.
The namesake Flicker was the first card to exile and immediately return the target. This is where the mechanic got its unofficial name.
The creature that returns is a whole new object without any relation to its previous existence. That means that, for example:
- The creature will trigger all applicable "enters the battlefield" and "leaves the battlefield" abilities.
- If the creature you blink is being targeted by a spell or ability, then it will lose track of the creature and not affect it, or will fizzle if that creature was the only target.
- Auras and equipments attached to the creature will fall off of it, and counters get removed.
- It will return untapped.
- All temporary effects, such as from Giant Growth or Death Wind, will be removed.
- The new creature has no damage marked on it, so it's like an improved regeneration effect.
- If you blink the creature during combat, it will be removed from combat and will neither deal nor take any damage, but (if it was already assigned as a blocker), the creature blocked by it will still be blocked.
Other blink cards such as Flicker can also target enemy creatures (though not at instant speed), which can be a very valuable play at the right time.
In short, blink effects are a powerful trick that can throw a wrench in your opponent's plans at a crucial moment. The +1/+1 counter for spirits is more of a bonus in most cases, but of course it allows you to get even more utility out of this spell.