What version did you upgrade from? Were your spatial views previously registered with the geodatabase or is this a stand-alone instance?
Spatial views (Query Layers) do have additional overhead when compared to feature classes or tables.
It sounds like you would have had them registered at 10.0 using either the sdelayer -o register or sdetable -o create view. Does that sound familiar? If so, that might explain the performance hit you are seeing at 10.3.1 with views after recreating them.
To address the performance you may want to consider using the SDE 10.2.2 command line tools to register your views at 10.3.1.
Thanks for your response Christian. Turns out that the issue was within the MXD itself. Legacy MXD didn't know about "Query Layers". Once I added the views back in to the MXD as Query layers everything was right in the world again.