Mr Goldfish
Shotgun mics (often used on a boom) are indeed directional mics. They pick up sound in a very narrow angle from the mic. This doesn't mean you will necessarily get only the sound you are looking for. If the mic isn't utilized correctly you can get some strange sounding/useless stuff.
The idea is to capture the cleanest dialogue possible with these mics as they have the potential to single out individual voices from the mess of background. This dialogue is then combined in post production with sound effects (such as footsteps etc) and usually some (stereo) background sound that was recorded before the shoot. So you get all the sounds you need but you can tweak each individually giving you much more control.
I don't think I have ever heard of the click, pop sound thing. Sorry. Sound isn't my specialty.
A boom mic is really the only way to get clean dialogue. You can get some good stuff with wireless lavs but these are often "omnidirectional" so they will also pick up any other sounds that are close to the mic. The boom method is pretty much the standard.
You can, of course, record dialogue separately after the shoot. This is called ADR. It can be a pain though as you have to perfectly sync the sound to the image.
So your best bet: use a boom mic