Not a waste of time at all. The short answer is the Links functionality was originally built without the ability to be extended beyond how it works now. Within WordPress core (what the "WordPress.org" version is called that is the base of WordPress.com, as well as what runs all non-WordPress.com WordPress sites), the "posts" feature became more and more powerful and able to be extended relatively easily. For example, on themes like Stay that has a hotel rooms listing option or Panel with a separate "comics" section, both of those pieces are actually just "custom post types" (CPTs), or posts that are internally designated to be something other than a normal "post" or "page".
Between CPTs and the Custom Menu functionality, the Links functionality could be done served better by one of those, so it made sense to begin the process to retire the code in WordPress core.
That said, we (the broader WordPress.org open-source developer community, not just WordPress.com) don't want to cause things to break. When Links were removed from new installs of WordPress.org, it continued working without issue on older installations. Even the code for Links was left in WordPress.org completely, only disabling it, so it would be relatively easy to enable it if desired. If you're running a WordPress.org site, you can install the Links Manager plugin, which is actually, for now, just one line to re-activate the dormant code.
In the end, the idea is that eventually the code would be removed from WordPress.org and exist all within the plugin, so folks who want the Links functionality would still have it while keeping the core product "lean".
The Links functionality hasn't been removed into a plugin at this point. I can't say with certainty what the end result will be, but I don't foresee WordPress.com removing the feature if it is only a matter of enabling the plugin internally on our end to have it work.
Perhaps a bit too lengthy of an answer, but in short, while the Links functionality is "on the way out" in the broader WordPress world, there is no current plan or timeline to remove it from WordPress.com. Hope that helps!