There are many factors to consider in something like this (like the computer and other IT resources, to configuration/settings), so I'll start with some general information.
When you interact with tools and other elements on the canvas, even though you're not pressing "run", there are still things that Designer is working on for your user experience.
For the query example, before you run, it might check to make sure the database specified is valid and accessible (among other protocols). Also if you have a "data preview", that adds a query the first few rows of data. Depending on your connection to the database, these simple requests could take a few seconds to communicate. In my work, I notice a significant difference in database latency when connecting to a local database here in Fort Worth, TX compared to Amazon hosted resources in Virginia.
Another thing the Designer canvas does by default is populate metadata in the connected tools (whenever possible). So when you add a Select tool, it will populate all the fields and their types without re-running the workflow so you can start working right away on that newly-added Select tool. As you can imagine, the amount of metadata to keep track of can really add up with more tools and more field involved. So working with more and more tools will increase the time this takes.
Now I do have a solution for the second problem, but it comes at a cost. In your User Settings you can disable "Auto Configure". When this is off, the metadata will only be refreshed when the workflow is run. So if you add a Select tool, it will be empty until the next run. This can add a bit of challenge to your Design process, but if speed is a priority, this is a handy feature to be aware of.
Hopefully this shed some light on your situation.
