If those stock agencies work on file size, rather than resolution, that's, frankly, nonsense. The size of a lossy compressed image (such as a JPEG) depends on various things - the number of pixels, the amount of detail in the image, and the amount of noise. Remove the noise, and the resulting image is simpler - so the file is smaller.
They can't have it both ways. Making a 3MByte JPEG from an 8-10 megapixel image means that the quality slider is pushed way to the right - and there wouldn't be an appreciable drop in quality if you backed it off a bit, even though you're getting significantly smaller files.
I think you might have misunderstood - unless there's some reference somewhere that I missed out on. For example, Fotalia have this
on their web site - which specifies an ideal resolution (at least 3000 x 2000 - 6 megapixel) JPEG with minimal compression. That doesn't mean any compression is bad - but you don't need to be after 3MByte JPEGs each time, as they're probably undercompressed.
Noise reduction programs can hurt the detail in your image; that's a side-effect of the way that they work. One way around this is to put the noise reduction on another layer, and mask it for surfaces - so that you only noise reduce the surfaces, where you most notice the noise. Certainly the 'professional' versions of some of these programs (I use Noise Ninja Pro Bundle) have a Photoshop plug-in, which makes this easier to do; the masking can be done with the (free) TLR Professional Mask Toolkit
.
However, it's better to avoid the noise in the first place if you can - which means choosing a lower ISO. That, in turn, may mean adding light to your images and/or using a tripod. Noise reduction is the last option if you're out of other options and have to choose high ISO (such as indoor shoots where the light isn't that good, flash is either prohibited or you need ambient light for correct background exposure, you've done all you can with a fast lens and either a tripod isn't feasible or a slow shutter speed is undesirable).
I look forward to noise reduction plug-ins for Lightroom - but that will have to wait until Lightroom's SDK is released. It may just happen with Lightroom 1.1, but I'm not holding my breath. It would also be good if the plugins were enhanced to work as Smart Filters in Photoshop CS3 - but that certainly hasn't happened yet for Noise Ninja.
David