I assume you are asking about using HTML articles.
1. There is no limit beyond simply keeping things reasonable.
2. Yes. Just use navto://articlename
3. Yes. I've used min-width of 768 and max width of 1024 to control it.
4. InDesign does not enter into any of this with the exception of using the folio builder panel. Everything else is done in Dreamweaver or whatever program you decide to use for the article.
If you want to restrict the HTML articles to one orientation or the other, use the _h and _v suffixes.