If I am working only with lightning and do not use visualforce at all should I wait for the developer certification to be updated? I mean, will they totally exclude visualforce (or make it at least deprecated) in the near future?
Your question is too broad, but here's an attempt to provide an answer to it.
To start with - Visualforce is not going away. It's a different framework to build "server-centric" applications. Here's an excerpt from trailhead where you can validate this:
First, know this: Visualforce isn’t going away. Your Visualforce code will run on Salesforce for a long time to come. You don’t need to convert existing Visualforce apps, and you don’t need to stop creating apps with Visualforce.
As for your certification approach, you may not have a "working experience" of everything in Salesforce considering its so vast and that you don't get a day to day use case to implement each and everything but choosing a certification path lets you explore the platform feature, learn about those and then be able to apply those practically.
This is not applicable only for a developer certification but for any other certification and the topics within those certification. I have had scenarios where I never say used validation rules (just an example) but still I knew about it and that when it can be applied, which helped me to understand the platform capabilities and thus enhance my knowledge around it and address questions in certification.
My recommendation is that the more you learn is more you gain, as we do on this platform!
No. They will not totally exclude or deprecate Visualforce anytime soon. There's quite a few documents online that you can google to reference we have also answered this question a few times on this forum.
Visualforce is not going to be replaced or deprecated for the foreseeable future. If you want to get certified you should definitely learn Visualforce and get certified.