Acknowledge somebody whose advice is not relevant to the current manuscript anymore?
How to decide who to include in the acknowledgements?


Generously.
If people gave up their valuable time to help you in the process of developing that paper, it is kind to acknowledge that.  This is true even with contributions that are very helpful but may not be directly reflected in the final text, such as avoiding a long rabbit-hole or programming for some data collection or analysis part of it.
Per Mad Jack's answer, you can have the acknowledgement accurately reflect that the contribution was to an earlier draft, or whatever the contribution was, but they still helped.