In reply to Is Indesign the best for me (or Publisher):
I'm a graphic designer. If you want to do serious page layout, InDesign is the way to go. InDesign gives you enormous control over your layout. The downside is that it's expensive and has a considerable learning curve. I can't compare InDesign to Microsoft Publisher because MP is not a program that I use (and I doubt if any graphic designers use it).
Table of contents — Yes you can set it up do update automatically. For a short document it might not be worth the trouble, but for a big document it's a big timesaver. However a beginner might find it a little tricky.
Layers for different languages — Yes, that's often done, but keep in mind that different languages may run different lengths.
PDF Links — Yes, you can save your InDesign document as an interactive PDF containing links to specific places in the document and/or links to external sites.
2 versions ? — No, you don't have to create one version for PDF and one version for printing, and I generally don't. But there are a few situations where it might be a good idea. For example, if your document is going to make a huge (file size) PDF because it's really long or has a lot of graphics, that can be a problem if you want folks to view the PDF online via their browser. (Not downloaded, but viewed in the browser.) In a case like that, a shorter or less graphic intensive version might work better for the PDF. Another case is a large-format piece, like a poster, that would be awkward to view as a PDF as you might have to zoom in a do a lot of scrolling to read the PDF. But generally speaking you can just save the PDF from the same files used for the print version.
Some general advice — if you're not experienced in InDesign, a big catalog might be biting off more than you can chew. You might want to consider hiring someone who's more experienced to help you set up the files and lend a hand if you run into problems. Preferably someone local so they can demonstrate things for you.