It's been some talking about that regarding the EG shoes. EG claims it's bad for the shoe as moisture from your feet cannot ventilate through the sole that has a extra lay of rubber. But I just think they want your soles worn faster and get that extra cash on a resole job. Also, if you do the whole resole job why do they care? They will remove the whole sole anyway and put a new one.
I was topying the soles all my life without such problems.