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We do not manage the Download IDs ourselves since Joomla! 4.0. They are now managed by Joomla! itself.

The Download IDs (or Download Keys, as Joomla! calls them) are stored in the #__update_sites table, together with the URL to the update site of each extension.

These records, or even just the Download Keys, do not get removed by themselves. You'd have to delete the update site record, use the Rebuild button on the Update Sites page, or have a third party extension removing the #__update_sites records itself. Other possible issues would be restoring the site to a state where it does not have the Download Keys, or the host doing the same for at least this database table.

I have not experienced this issue across a dozen of Joomla! 5 sites. I am talking about development, testing, and live sites across a different mix of Operating Systems, platforms, and hosting providers. Nor have I heard of anyone else having this issue. So, no, I do not think it's a Joomla! 5 issue at all. Besides, I can and have read its source code. There's nothing in there which would remove your Download Key except a. deleting an update site or b. using Rebuild. Note that I have contributed the original version of the Update Sites management page, I had fixed the Download Keys feature when it was merged back when Joomla! 4 was beta, and I have code reviewed the rebuild feature. When I tell you there's nothing there to do any weird crap, there's nothing there to do any weird crap. I can guarantee it. That's the beauty of Free and Open Source Software; we can code review it so there's no "what if" possibility surviving our scrutiny.

I would posit that the problem lies either with the hosting or, most likely, using third party software. You said that you are not using any third party software on any of them... but you are using Akeeba Backup Professional at the very least which is a third party extension, right? :) So, just based on that, I would say that you have the wrong idea about whether you are using third party software. I would also assume that you are using a template and/or template framework at the very least – there are very few of us who go into the trouble of making a template from scratch.

At the very least you need to catalog the software you have installed across all of your sites and find which ones are common. Remember, third party extensions can be components, modules, plugins, or templates. All of them have executable code. Yes, even templates.

You also need to check whether there are any CRON jobs you might be running, beyond taking a backup. I've seen a site which was having periodic issues and the problem was a CRON job intended to delete temporary files which unfortunately went a bit further than intended.

If you are using a third party service to monitor your site you might want to check if you have provided your Download ID in their configuration. As far as I know, they do replace the Download ID in Joomla with whatever you have configured with them.