The reason institutions delayed smoking has nothing to do with RCTs and everything to do with regulatory capture and corruption. Even in the presence of RCTs (which wouldn't be ethical, of course) this still would've happened.
That RCTs have failure modes does not change the fact that they are the best we have in the face of confounding variables - they simply require good design. This claim about Tdap is not like smoking...we don't have the same understanding of the underlying biology nor the massive effect sizes from other studies.
I have read the Book of Why and Probabilistic Reasoning in Intelligent Systems. There is nothing within those books to indicate animus against well designed RCTs. Rather he advocates, as I already did, for intelligent combination of sometimes sparse RCTs with the large N of observational studies.