My view may be a bit off because I have only ever used scrubbers with the high sides. My experience with them has been in a few different facilities producing a few different products. They are good, and they look good to those from the outside coming in to see your facility. However if you expect them to completely remove all debris I think you will be let down. I don't think any boot scrubber will every time. In the wet facilities they seemed to do a pretty good job but nothing really ever had time to dry on the shoe. In more dry facilities I didn't think they worked as well. Overall I don't really think having the sides will do a whole lot for you but that may also depend on the facility and production conditions.
Maybe just verify that the SOP for using the scrubber is being followed? Perhaps people are just running through it and not taking the time to let the scrubber do its thing.