The A-12 and SR-71 were flat like an ironing board for a reason. This way, the pitching moment at Mach 3+ was easy to calculate. At the time of the design, Mach 3 wind tunnels were rudimentary and had super small test sections, so their results were unreliable. Indeed, most work was done with intuition and slide rules. Calculations were done by rooms full of human computers because digital computers were rare and complicated to use (did you ever try to sort a deck of punch cards after you accidentally dropped the metal box which held them to the floor?). Granted, these computers were miles ahead of the digital computer that was used in the wing design of the Messerschmitt 262, but there was little existing software, so if you needed a quick result, those human computers were the way to go.
While today much computation removes around iteratively solving large systems of equations, where each equation describes the state in a tiny speck of a large, there-dimensional grid, back then much was done with differential equations which were solved once for a complete system, be it heat in an engine or lift on a wing. Much data was tabulated and only had to be looked up, but this worked only when you stayed in the realm of tried and tested parameters. For new materials and Mach numbers, development was a combination of basic research and trial and error. To give you an impression what was available for flow parameter calculations, look at NACA report 1135, published in 1951. I'm sure papers like this piled high on the desks of the Lockheed engineers of those days.
But those engineers had much more time to try and learn the new stuff. Meetings were short and to the point, bean counters and lawyers still saw themselves as supporting staff and not (yet) as the center of the company, so much of the bullshit that is keeping today's engineers from being productive wasn't around yet. If you read the biography of people like Ben Rich, you will learn that years of experience from wind tunnel data enabled Kelly Johnson to guess the peak temperature of a shock to a few degrees. I have worked with engineers who could tell you the lift curve slope of an arbitrary planform to two digits after the decimal point simply from looking at it.
With the F-16 much had become different already. Powerful and flexible computer codes allowed to replace wind tunnel research and made complex curved surfaces possible. If you look at the supersonic drag of the clean F-16, you see that the shape of the airplane has been optimized for trans-sonic flow. While the drag coefficient of older designs had a clear peak between Mach 1.0 to 1.2, the drag coefficient of the F-16 stays roughly constant over the whole supersonic range. This is the result of careful tweaking that would had been impossible in the times of only wind tunnels. Also, the belly intake is the result of lots of experience, not only from aerodynamics, but also from operations: Earlier generations of engineers were too afraid of FOD to accept a belly intake.
While today's mechanical engineering graduates have again vastly better tools available to them than the team around Robert Widmer, they will lack all of the experience that comes with having contributed to the development of several airplanes. The result will be respectable, but fall short in many details where experience made the engineers of the 1970s pick the overall best solution.