In general using the dashboards to configure SmartApps (which is what they all are under the covers) is going to give you more flexibility in most cases. We see SmartApps that you install from the SmartApp Catalog as more of the unique and niche use cases or if you write your own. In the end, it doesn’t really matter, it is just where you want to set things up and administer them in the future.
The benefit for the Dashboard ‘apps’ is that they are usually flexible and also usually have a nice clean step-by-step process for you to walk through to setup and install them. Dashboard apps are also relatively recent. Prior to them everything was done via SmartApps, which is why you see some SmartApps that do basically the same thing as Dashboard App. SamrtThings or others wrote those apps before you could do Dashboard Apps.
SmartApps, on the other hand, offer more complexity and non-common usage. For example, I just wrote a SmartApp that works with my Ubi. I can give a voice command to Ubi, which makes stuff happen in SmartThings, which checks that my doors and windows are closed, then shuts off lights when I go to bed. This would be a pain to do in the dashboard as it involves sensors, lights, virtual tiles, and some code work. But it’s relatively straight forward for a SmartApp.