It depends on how the spell manifests
Detect Evil is not a Scrying spell, though it has a chance of working through one (emphasis mine).
As with all divination (scrying) spells, the sensor has your full visual acuity, including any magical effects. In addition, the following spells have a 5% chance per caster level of operating through the sensor: detect chaos, detect evil, detect good, detect law, detect magic, and message.
In that case,
A creature can notice the sensor by making a Perception check with a DC 20 + the spell level. The sensor can be dispelled as if it were an active spell.
By itself, Detect Evil provides no saving throw for a possible detection or counteraction. The spell description also does not mention any light, sound, sensation, or other kind of detectable sense.
More generally, if the spell describes nothing detectable manifesting, your target won't be aware. Evocation spells have spectacular manifestation of their spell energy, while Illusion spells could completely obscure their manifestation (to avoid disbelief).
Now take Message for example. It has a duration of 10 minutes, before which you have to appoint your targets. But as long as you do not whisper any words to these targets in those 10 minutes, they have no way of knowing they are being targeted by Message. Like Detect Evil, the spell description does not mention any light, sound, sensation, or other kind of detectable sense. Message does not provide a saving throw, nor is there a spell resistance.