Linux

I don't think I've used JDownloaded since I upgraded for dial-up. Like, download managers as a whole have become mostly useless and not even that reliable. Used them all the time on dial-up since it took so long to download, you just had to.

We no longer need parallel downloads because web servers have become much more reliable, and nothing really takes more than a couple minutes to half an hour to download so being able to pause and resume just isn't that useful anymore. Chrome and Firefox now also support stop/resume natively and it works most of the time. But again, why use a download manager when a 5GB ISO takes less than a minute to load up in Firefox.

And all the piracy long moved to torrents which also does all of that and then some more.

Distros package things by demand. There's no demand. Some older software might be in the repo because they were popular 10-20 years ago and maintenance is basically, just change the version number every now and then. And even then, Arch somewhat regularly kick out packages from official repos to the AUR when they become old and a maintenance burden.

It is in flat huh I think

Despite it being one of the most popular [...]

It's only popular among people who download frequently from filesharing websites. Most Linux users don't, hence why it's not available on any of the default distro repos.

In fact, I'd say the act of downloading regularly from filesharing websites, has largely gone out of fashion among the general public (obviously I'm ignoring the underground/illegal/niche scenes here).

For the most common types of large files which Linux users might manually download - eg ISOs, movies, TV shows - torrents are generally preferred, and torrents have very capable native clients already, such as qBittorrent.

For other general large files manually downloaded via http (eg Linux ISOs, tarballs of packages etc), these are already hosted on legitimate websites (like github) which don't impose any artificial download restrictions, so your browser, or any "normal" download manager can handle them just fine. For these sort of downloads, aria2 is the most popular third-party downloader in Linux. aria2 is a command-line program, but there are many GUI frontends for it too, such as uGet and AriaNg. There are also browser addons that integrate with aria2. Aria2 is also native and very lightweight, so again, there's no need for JDownloader here.

TL;DR: Most distros don't offer JDownloader because most Linux users don't actually need it.

It's unmatched for some of the things it does and sites it supports, but I think it's a nightmare for any distro or package maintainer. It wants to manage its own installation and updates, at the user level, pulling in who knows what code or binaries.

I think that makes it mechanically hard to handle, verify, or trust.

I just looked it up and the core is not foss

I would guess because if you compile it from code no everything is included. There are some proprietary addons that are not included in the source code but are in the binary release.

Pure speculation:
I think it's just not that popular. Does it do something more than rclone or simple rsync? If not, then its main selling point would be GUI. But then, I think, either one can use the remote location via their file manager (like thunar with MEGA for example) or there is not that much difference between opening another app and using web. And if the selling point would be pausing and resuming download, torrents are probably more verstile
It is available in AUR, though, so maybe it's only me that haven't heard about it earlier

Also, it's a java application. There is not much to package or depend on, I guess

Not sure really; it may be because either jdownloader has a self updating function (i dont think its this one because it could be patched out like most repos patch telemetry out of audacity) or because it has very frequent updates to keep the site scrapers and downloaders working since it's a continous arms race between them and the websites ( i'm not sure if repos have nightly builds of programs or not).

It's on flathub