Generally speaking, lower light levels or faster exposure increase saturation. Try it with a flash. Throw some kind of coloured filter over the front, shoot at full power, then gradually bring it down on each shot. You'll see an increase in saturation as the light goes down. Remember, saturation isn't the same as brightness. More light will obviously produce brighter colours, but not necessarily "more colour". Eventually, no matter how dark, if your exposure is too long for your chosen ISO & aperture, it will still blow out.
Depending on what you're trying to achieve, longer exposures with ND filters over the front can produce some very neat effects. A cool trick doing this is to help get crowdless streets. On a long exposure like this, if you have a few people walking through your shot, because they're in the same place for such a relatively short space of time, they don't register on the shot.
I did a shot at the Shambles in York like this. Ended up throwing on a 2 stop polariser on (I didn't have an ND filter handy), f/22, ISO100, and ended up going with about a minute exposure. At least a dozen people walked through my shot in that time, but none of them showed up in the final exposure.
I read about somebody doing this back in the film days with about a 20 minute exposure and whole bunch of ND filters, and the results were incredible. I just had to try it out.
You pretty much answered your own question.
Throwing any extra glass on the end of your lens (even a perfectly clear UV or skylight filter to protect the end lens element) is going to degrade the image quality to a degree. It might not be noticable until you load it up into Photoshop @ 1600% and do a direct comparison of an identical shot without a filter (it may not be noticable to your eye even then), but it will degrade it. How much it degrades depends on the quality of the ND filter, and the reliability of your body. It may degrade the image quality no more than the random fluctuations in your body's sensor anyway.
The long exposures hasn't been something I've had a chance to try out recently, so I'm not sure what the best prices are for really good ones, but I am getting ready to needing some soon, so I'll probably start my quest looking at B+W and Hoya Pro ND filters.