Welcome! Picking up HC97 without prior Harpoon experience probably puts you in the minority but it was a great game that just happened to get improved in more recent iterations.
1. Yes, and with the recent uptick in inquiries, I reached out to the powers that be today, received a response that it is being looked into (so good job bringing it up again everyone) and hope for a response in the next couple of days. There was certainly an expectation a few months ago that the more recent Harpoon Classic would be re-released like HC97 was re-released.
2. Some of them will work with HC97 but many do require the Matrix edition. It will help to try older scenarios first. On GIUK - HarpGamer page for instance, the ones that mention EC2000 should work with HC97, the ones that say EC2003 will not.
3. For the old-timers like me the answer is very long and complex involving intellectual property rights, personalities, fundamental disagreements on what drives a realistic outcome, ... However, an easier answer is that for many players HC is just more enjoyable. Command is amazing in so many ways but the reward is gives me doesn't compare to HC which aside from Civilization may be the only game that can keep me so engaged that I find myself putting off bedtime just one more hour right up until my alarm goes off for work.
4. Very very different. HC97 follows the Harpoon 3 paper rules for the most part however it uses an adaptation of the Harpoon 4 paper sonar model. For the post-HC97 builds we weren't allowed to use the Harpoon paper rules (politics!) so when algorithms were replaced they tend to be my creations. Where we tweaked things (such as sonar), we attempted to make the results come close to the Harpoon 4.1 paper results without copying the data and rules themselves. You can often find a copy of H3 paper on eBay (GDW Harpoon 3).
5. The tutorial is a good start, hopping on Discord (link at top of forum) and chatting with the gang with questions can be helpful. The command card made by a player will become one of your best friends Keyboard Commands, by location - Tools/Mods/Docs - HarpGamer