All the answers so far are exceptionally detailed, but I think the general takeaway is more important - you effectively have two choices:
Speak with the player and explain why letting monsters eat you is a good thing for fun (realism and the fact interesting stories rarely occur when everything goes right).
Shoot the player in the kneecap with an arrow (metaphorically speaking - disable or limit their ability/desire to use the power).
Option 1 is self-explanatory and most likely the preferred option. Depending on the relationship, I might even explain why I personally found the behavior frustrating. Even if you have spoken with the player before, that isn't always the same thing as clearing up a situation in my experience.
That said, it sounds like Option 2 is your best bet.
I am aware of the Undetectable Alignment spell and while this is a great asset for keeping surprises, it doesn't stop the annoyance of him constantly checking every NPC/object anyway.
Then you must give him a reason not to. He sees using the ability as a bottomless advantage. You must alter this perception if you can.
Altering the rules is not a good option, I believe, since this is obviously a one-sided unrecoverable disadvantage and may come back to bite you in other ways (e.g having your house rule used against you somehow). Having him suffer an in-game "curse" of some sort (outside the complexity of casting and NPC hostility) would be my preferred method.
As mentioned elsewhere, this could be as simple as a limit on daily usage or more serious (but creative) effects. The upside is that, depending on the effect and reasons behind it, this could offer expanded opportunities for role-playing.
"Curses" don't need to be directly magical in nature, either -- besides divine blessings (or taking away of that favor), the character could suffer a physical "curse" as well. Perhaps that sprained pinky never healed right and now there is a %50 chance the character is really casting "Detect Good" (for "Detect Magic" this could just be a failure to detect an aura properly).
Also, since you mentioned you felt this might be a symptom of character paranoia, perhaps the paranoia is real and the sufferer becomes "worse" when certain abilities are used to "feed" it. This could be anything from false positives (everyone is evil and every item is magical) to actual hallucinations (that guy has a concealed crossbow!).
The drawback of cursing a character is that the player may still feel singled-out and upset at this treatment. Because of this, "beneficial curses" might be a better option. Essentially, you offer the player a benefit for reducing his usage of a particular ability.
While the benefit of course doesn't necessarily have to be related to the suppressed ability, since he REALLY likes to detect things, perhaps NOT detecting things for X hours/days would yield a significant advantage to him (he can detect things that are normally undetectable, etc.). For extreme cases, the ability could be disabled/removed temporarily or permanently. Magic reduction or suppression could come with advantageous items as well.
Of course, any "curse" would need to be selected carefully (to avoid hurt feeling and so other portions of the game don't unravel) but this option also opens up story line possibilities as well.
...And Your Damnable "Detection"!
From a GM perspective, I find it somewhat grating when it's impossible to throw in any magic/evil as a surprise[...] Should I learn to adjust as the player is technically not doing anything wrong[?]
I believe the answer is yes, in a couple ways.
First, abilities are there to benefit the player. So at the heart of it, there SHOULD be situations where powerful magic or evil can be discovered and earns an advantage.
Secondly, it sounds like there is a note of infallibility about the detection.
Having cursed lands where everything is essentially evil (or simply doesn't work the way one normally expects) are valid options. But also remember not all NPCs/creatures who might take adverse actions against the PCs are themselves evil (they may be puppets or simply misguided).
Likewise, "evil" is an acquired state in many cases -- corrupting influences (magical or emotional) often take time to accrue before a creature is truly "evil" as a distinct trait. That doesn't prevent actions which others might perceive as evil along that path.
On the mechanical side, remember that spells and spell-like abilities (minus V/S/M and some casting time disparities) are subject to suppression or negation, at least for areas (and frankly any evil NPC worth her salt will likely take some pains to conceal the fact they have an evil aura).
Supernatural abilities don't function in anti-magic areas. Likewise, other magic or deliberate suppression might make detection impossible or flawed for magic auras.
There also may be other hindrances. For example, despite being at will, paladins can only concentrate on one person or object at a time. Depending on selection and situation, this could be a real disadvantage.
The bottom line, in my opinion, is that not detecting something doesn't mean it isn't there (and thus potentially allows for "surprises").