I think it definitely makes sense since it's still the best Google has to offer in the "pro" tier.
It's not a technical problem, it's a commercial one. If Google can't ship a model to replace the one they deprecated, that tells you everything you need to know about choosing a Gemini model for whatever you're trying to do.
That link shows 3.1 pro listed as deprecated with no replacement model.
Just like 3.7 Flash, 3.1 Pro says "No shutdown date announced."