I don't see anything that appears to be an application that depends on the pi-meson like some of the other particles.

Originally Yukawa Hideki predicted the pi-meson while lecturing at Osaka Imperial University in 1935, this is somewhat ironic considering in 1939 the Manhattan project started. 

General Groves must have known about Yukawa Hideki's work on the atomic nucleus, which was right up the ally of research of atomic power. I am wondering if he was concerned about his "enemy" having this knowledge.

It could be the case that the meson has no practical use in the development of the chain reaction and construction of the Atomic Bomb and perhaps has no apparent practical application thus the motivation for the question.