If you're close enough to be detected by the naked eye, you've already messed up. While the ships we follow in Star Trek are exploration ships, they shouldn't be landing on planets or needing to get in close to see what's going on. They hide from primitive planets by parking way outside visible range and using their Very Good Sensors to look around.
Now, all else being equal, having that last layer of protection could help. (Not just in first-contact situations; the Wrath of Khan fight, for example, came down to visual identification.) However, there are downsides to making yourself hard to see. Specifically, you are now hard to see. This could cause trouble when rescuing a ship, flying in crowded areas, or even when landing a shuttlecraft. (Imagine hitting a nacelle strut while coming about in a shuttlecraft.) There are probably disguised ships specifically for getting close to primitive planets, but we don't follow those ships around.
As requested, [the Wrath of Khan scene][1]the Wrath of Khan scene:
Sulu: Phaser lock inoperative, sir.
Kirk: Best guess, Mr Sulu. Fire when ready. [1]: