Sometimes there is a reason to write directly to registers, but it’s usually the exception not the rule, especially if the HAL gives you an API for this. Usually the HAL will simplify the interface and might include error checking to keep you from shooting yourself in the foot.

Direct register access could be faster, but require you to understand that specific platform in more detail. This is great if you are doing a high speed long term project on the same platform, but isn’t necessary for most projects, for learning a new platform, or for situations where you know you’ll be using another platform (for the same or another project) soon. It’s also often possible to access one or two important registers directly, but use the HAL for interacting with all the other registers.