My understanding is that they do in fact have end-to-end-encryption between Zoom clients, it's just that when you join via a dial-in phone number, the connection is (of course) not encrypted between your phone and the system you're dialing into. People who wanted end-to-end encryption could just choose to not dial in by phone, and they'd get it. (People who want end-to-end encryption between phone calls from unmodified phones want something self-contradictory.)
I'm not sure I'd call that "They didn't have end-to-end encryption." Would you say that my IRC OTR session with my friend isn't end-to-end encrypted because I connect to irssi running in a screen session on a remote host and the e2e doesn't go all the way to my laptop?