My view is, the shoes are quite effective at dropping "natural" times, but not as effective as EPO. It would make sense from a logical standpoint. Presumably, runners haven't gotten innately faster in recent decades - we're still dealing with the same old home sapiens.
So let's say, hypothetically, that without drugs or super-shoes, the very best runners in the world were capable of 7:35 to 7:40 for 3000m, and there were usually a few guys active at any given time who were capable of that. Well, here's what we might say in 3 different scenarios:
No drugs or super-shoes available: fastest time each year is in the 7:35 to 7:40 range, because that is pretty much as fast as a human can go.
EPO but no super shoes: fastest time each year in the 7:20 to 7:30 range, depending on drug testing, drug supplies, super-responders, etc.
Super shoes but no EPO: fastest time each years in the 7:30 to 7:35 range (I'm just going with a conservative 5-second improvement purely from the shoes).
But in today's era, we know we have the super-shoes, and we suspect PED use still abounds, but not as effectively as in the EPO era due to improved testing. So nowadays, you get all the benefit of the super-shoes, and a little bit from drugs.
I'm not trying to say this is definitely what's happening, because how would I know? It's not like athletes are publicizing their PED programs. I'm just saying it's not non-sensical to say that athletes are benefitting hugely just from having better shoes, even though many track WRs still stand.