the output to be 2 different PDFs from one set of Indesign files.
You can accomplish this by saving each PDF using a different preset - High Quality Print for the high res, smallest file size for web
but vector imagery would have to be rasterized...
You should be trying to keep all vector work as vectors. This, in most cases, lowers the file size. There are a couple of exceptions to that like if the vectors are very complex (layered etc) and you are using bitmap effects like drop shadows. In general, rasterizing will increase the file size and lower the quality.
Is there any functional difference between the 2 PDFs? I am wondering why exporting using 2 different presets will not do the job efficiently enough. You could always save your linked images with a low res version - same file but make a copy 100dpi instead of 300dpi. This might help but InD normally downsamples the images anyway when exporting as smallest file size.
EDIT:// In Acrobat, you can save as "Reduced Size PDF" which strips out all the meta data etc and makes the PDF lighter and faster for web use. This would be a final, before publishing online step.
The High Quality Print setting and smallest file size isn't fixing it. It is lowering the quality and resolution of raster images but doing nothing to vector graphics. In many cases the vector images are extremely complex (maps are usually the main culprit) and layered.
Another culprit is likely placed PDFs that are mini versions of other InDesign documents, like images of other products. These again are hi-res, and may contain highly complex vector images.
Probably replacing maps and some of these minis would help, but again adds a layer of complexity to our production that I'm trying to avoid if there is a better way of doing it.
We have utilized the reduced size option which has helped to some extent.
If you have a lot of complex vector graphics, just downsampling the images won't cut it for reducing the file size of a PDF. And Save As Reduced PDF doesn't give you any controls.
Here are two possible methods: One is to use the PDF Optimizer in Acrobat. I haven't used this myself but I saw it demonstrated recently. Choose File > Save As > Optimized PDF in Acrobat X Pro. In Acrobat 9, it's in the Advanced menu. Click Audit Space Usage to see where the file size is coming from.
You can reduce the size of the images by using the Images panel. But if it's complex Illustrator files, you may see an entry called XObjects (as I recall). Click on Discard User Data, and check Discard private data of other applications.
The other method is to take the PDF and rasterize it in Photoshop. The vector artwork won't look as good but if you're only viewing it on-screen, people won't be zooming in on it anyway.