Does having a bottom aerator/diffusers make a difference when applying herbicide? -- yes it can

Does the water movement lessen the effect the herbicide has if you are trying to treat certain areas? -- yes it can

Does the aerator need to be turned off -- no but it should be considered - possibly moved.

...or should you plan to just leave it on and treat the entire pond -- no as you could kill all the plants including the plankton and cause a DO crash killing your fish?