I have not the slightest clue on why they do hidden tracks. It could be that a lot of bands do them just because they've saw other bands do it. It could possibly even go back to records were you could play it backwards for a hidden message. I can think of one album though with a couple hidden tracks that basically trash on the record producer who released the album, so I'd say at least some do it to get material past that they don't what the record company seeing until too late. In some ways its cool, but in other ways its definatily annoying.
The CD I'm thinking about also had the songs on their own tracks, but 98 and 99 just like Ehlers was saying, with all the in-between tracks being 3 or 6 seconds of silence. I like the idea of having them just like all the other songs, just not listed on the album cover.
I also have a CD with several hidden tracks, however they were avertised and not every CD had them. And it would only have one, not both. So even if you got lucky, you'd have to buy the album twice to get both extra songs. So there's at least one case of it being a marketing ploy.