Beeper isn’t using Apple services (at least not in Beeper Mini, their new e2ee iMessage client), and thus is not subject to any Terms of Service from Apple.
They’re publishing client software, which is protected expression provided it’s original and doesn’t infringe any trademarks or copyrights.
The end users are the ones potentially violating the ToS by connecting to Apple APIs.
Apple has no basis to tell Beeper to cease and desist from the publication of software that it is legal to publish.