"It depends"...
If factory applied, I either:
-Weather over them if the weathering job is light. (i.e. a relatively newly delivered car*)
-Mask them for the bulk of the weathering -OR-
-Remove them, weather, reapply*
*I model the "Conspicuity Stripe Transition Era" so I may or may not reapply. Few cars would have extensive weathering over top of the stripes in my timeframe. I've experimented with the actual reflective stripes that I think a couple of companies make and I think they are pretty cool...recognizing they are extra thick but not caring too much.
I would prefer mfgs leave them off unless it is a car that was manufactured at a time where they were required and/or delivered that way. One other exception would be if the car also had extensive modern graffiti that was indicative of a later timeframe where the stripes were required.
EDIT: Just noticed you asked for a weathering "pro". My bad. I'm just an amateur.