The GBU-57A started service in 2011. Fordow was completed in 2006, Natanz somewhere before 2002, so there's a good chance they did not know that kind of bomb would be available.

While they could've said "let's just assume there will be something X times stronger than anything known", it would also have increase the price to build these facilities by a factor of X+Y.

I'm no expert, but I imagine once you have your centrifuges up and running, you don't want to continue setting of blasts nearby to add another sub-level to your plant.