They are also completely invisible for me (using DX11 Ext) so I assume that full invisibility is a function of DX11. It was explained to me some time ago that some mutants, NPCs and anomalies are intended to be fully invisible, and it is only a limitation of DX9 that allows you to "see" them. I don't know if that is true, but the game does provide ways around their invisibility.
Associate (behind the bar at the 100 Rads) will modify your PDA to show the location of Bloodsuckers and other mutants (or you can listen for the Bloodsucker's 'heavy breathing'!); invisible NPCs usually carry weapons that remain visible; and you have endless bolts to help you avoid anomalies, especially when most anomalies are harder to see during the day.
Not a great comfort, I know; but selecting DX9, DX11 or DX11Ext may be the choice that you must make depending on your personal preference.
Again, I am not very knowledgeable about DirectX and its versions, so please take what I say in that context.