The web is only a subset of hypertext so not everything you can do inside Storyspace is necessarily possible - or at least easily possible. Storyspace can export its notes to HTML (one at a time) but unless you need narrative hypertextual features like guard fields, I’d suggest Storyspace’s sister app Tinderbox is a better choice. Tinderbox post-dates (c2001) Storyspace but draws from it and since Storyspace v3, the two apps now share a common code base. The updated Storyspace v3 file format is readable by Tinderbox so migrating any data ought not to be problematic. None of this is a canard against Storyspace, simply that to write a website, it might not be the optimal tool.
My own reference about Tinderbox, aTbRef, originally my own Tinderbox file of notes about the app but now a public resource has been running as a website since 2004 and created entirely in Tinderbox (essentially from the same TBX file). So, big resources are possible.
This is currently possible in current Tinderbox but not (yet?) in Storyspace. As the two share a code base it is probably a matter of a Storyspace user writing to Eastgate and asking that the feature be added there. However, when that in-document link—be it note-to-word or word-to-word—is exported, the link target is the note. Long story short, though possible it’s a niche use for which the ROI on the extra engineering might not be ideal for Eastgate. But again, do write in to Eastgate (this being a user to user forum not tech support) and explain your need in this area.
As to your other questions.
#1. Depending on the complexity of the files (I did look on you website but can’t see them) I doubt it would be difficult to extract the content from the pages and implement them as Storyspace or Tinderbox notes, then re-export.
#2. Using Storyspace/Tinderbox you’d edit the source notes and re-export/upload the affected pages. If you want to edit the webpages then I think you want to start from a completely different place and move your old pages into a wiki or a blogging tool. IOW, put your notes in a web database-based tool. Of course if you want Storyspace maps that won’t help.