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The paladin is actually a Paladin of Luna, the Moon God. and yes, all my gods are homebrew. so the "paladin is evil" thing isnt really a problem .
 

The problem with A-Ha moments like this is that if you drop too many clues, the player will figure it out and react accordingly.  Too few clues, and the reveal seems like a gotcha, and that isn't any fun either.  Twists are cool when they make the previously chaotic looking jumble of information make sense, but they're really lame when they exist only to surprise the viewer.  There's also the question of what the "viewer" is since your player's PC is a flesh-and-blood inhabitant of the world.  

So, to answer your question, no I don't think that the Paladin's Detect Evil should work on an evil deity mascarading as a good deity, but I'd double check your premise, just to make sure it registers on the fun meter. 

No need to justify you hidding the Gods alignment by giving it a magic item.  If an evil god masquerading as a good god can't even hid it from a 1st level paladin then why is he even trying?  Just have his alignment undetectable by magical means, though his actions may give hints to those that are aware of them.  If the god being evil is a big part of the campaign, something that the players need to figure out before they can take significant action against the god, then dont share this with the players unless the character have seen enough to figure it out.

I do agree that these big reveling moments can be hard to design, because the clues dropped may not have been grasped by the players or are to vague, or the clues become obvious to quickly.  Or if it is over a long period of time maybe the players have just forgotten what the characters know, details do tend to fade away, especially if the story does not move forward quickly.

My advice here is to start with very vague or even confusing clues that might not make sense to the players.  I often create something to give the players, something that is tangible, this allows them to look back at things they have found in the past, and might help them to connect the dots on a picture that otherwise might be inperceptable when looking at the dots individually.  Start to give them clues that become more and more clear when you get towards the part of the campaign when you want them to know for sure.  If they figure it out earlier, then great, they can take action earlier against the god and his cult (see below).

Maybe they run into that cult of the god that betrays his true alignment, by claiming to follow the true god and acting in more obviously evil ways - but the players only get an inkling of the truth behind this statement because the rest of the world worships the good 'version' of the god, and might believe this cult to be twisted and wrong.  Then when the cult starts to grow in power, popping up in more places and begin to gain more influence in the world the players might start to think that they are the true followers and the god they believe to be good is in fact deceiving them and the rest of the world.