Yeah, but the demand in the 40s had a completely different pattern from today's demand, so you can't just ramp up train frequency across the system and meet it.
The L train to Bedford Ave carries way more people now than it ever did in the 1940s, when Williamsburg was a modestly dense working-class neighborhood. On the other hand, those letter lines to outer Brooklyn are much less used today than they were in the 1940s, as are parts of the system in the Bronx. And, of course, there were elevated lines over Second and Third Avenues in the 1940s.
The parts of the system that run at crush capacity are already running with the highest possible train frequency. Some of the lines might not seem maxed out on headways, but they have to deal with interlining; the frequency of the F train can't be increased because the line it shares with the E train in Queens is fully loaded, etc.