This was in the ‘60s when there were significantly less security issues.

There’s still a fairly large train station complex underneath the World Trade Center.

Probably not in 1960—Russian nukes would come from the sky. Also the Capitol already has a few tunnels underground.

Cities like London and Madrid actually have had bombs on trains. It's not a "security threat" to buildings above.

What is a security threat to infrastructure are roads, where you can drive massive vehicles into people, transport and explode bombs, etc. The Manchester bombing for example was a truck exploding parked on a public road.

If it was security, those concerns certainly weren’t shared at the Pentagon where the Metro entrance and exit were into the building for decades.