My personal experience is yes, they do restrict flow, even when they are perfectly clean. I don't know if current high-end guns have such strainers...my older DeVilbiss guns do not. I purchased an inexpensive gravity feed hvlp gun from Home Depot to spray some POR15 as I was nervous about putting that stuff through my DeVilbiss. On first use I noticed a paint flow significantly less than what I expected. It seemed like the gun was being starved of paint. Upon investigation, I found the gun had an internal strainer in the cavity where the cup screws on. I was surprised to find it as my other gravity guns did not have such a part. I removed it and the gun then sprayed much better. Here's what it looks like after removal:
Notice the "snout" to the right of the screen area. That snout protrudes through a circular opening in the gun recess that is not much bigger in diameter than the spherical bulb at the end of the snout. That fact alone, creates an annular area for paint to flow through that is significantly less than the full circular area of that opening. While that snout may be a way of metering maximum flow to the tip to keep it within the capacity of the air cap to atomize properly, I had no problems with atomization without that strainer in place and using the recommended maximum air pressure of 40 psig stamped on the gun handle. In my opinion, the gun works a LOT better without that strainer, plus it's one less thing to bother with during gun cleaning. Use of the cone filters when filling the cup in the first place eliminates any need for an in-gun strainer. I don't know what others do but I leave that internal strainer out.