I think you should encrypt this, because of profiling data leak, this information can contain the time of chat between two clients (even they delete messages) and it's very good for branding, you can say you have the fully encrypted application. but to determinate the actual risk you need to ask your self, with that information like "message ids" what you can get about the user, when I say you I mean every person with access to the database and server. can you find out the message from who and for who? if yes its data leak risk.
about the signal app you according to this link they have data leak in the desktop application(but they send text body in notifications its nightmare) but in your case, you don't send text body to the clients.
according to whats app faq: your messages, photos, videos, voice messages, documents, status updates, and calls are secured from falling into the wrong hands.
its seems they don't encrypt notifications. but zulip mobile encrypt notifications