One important thing to keep in mind is that the EPS foam has very little structural strength by itself, so the thickness of the foam blank really doesn't contribute notably to a board's structural strength and durability. However, in a recent discussion that I had with Mike Zajicek, he indicated that there's often quite a difference in the density of ESP. Although the specified rating of the manufactured foam might be the same, the actual density and weight of different manufacturing lots can vary quite a bit. That's one of the reasons why the overall weight of boards can vary by plus or minus 5-6%.
So, depending on the actual density of the foam used, it can have an affect on the long term durability of a given board. I have found this to be true with a few of the custom boards that I've owned. All the boards were built by Zajicek, so the construction integrity was always extremely high. Over time, the beating a board takes on the bottom below the footstraps, and on the deck in front of the rear strap(s) can literally crush the ESP foam under the divinycel and laminations causing an internal separation and softening in those areas. I should emphasize that this softening occurred after 4-6 years of hard use, but it never has resulted in breakage or leaks of any kind. Other boards, which were used for far longer never reflected any softening of any kind.
To summarize my thoughts a bit, the thickness of the foam means very little with respect to board strength, but its actual density means quite a bit over the long run and can affect a board's overall strength and durability.