Well, the aerodynamic advantage is not always the 1st reason for short lenght exhaust designs. The race teams or companies who study and use these setups, to design exhaust the 1st rule they keep in mind is the power output over the aerodynamic (it's more in F1 where they match car aero and exhaust output to take most of the two).
The teams/companies who have real experienced engineers and experts on this "balck magic" which is the secrets of real race exhausts,
usually use the short exhaust designs taking as priority point the engine power. In some race categories or cases, it's true they combine "aerodynamics" with "engine power given exhaust design", so one of these two points can achieve a superior level of priority over the other.
The type of cars which use these short exhausts, also use front splitters, under-tray panels and rear diffusers, so the underside flow is not a big issue when they use rear exit exhausts. In some cases at the rear diffuser there is a combination of low pressures (exiting the under panels of the race car) finding the higher pressures at the rear of the car. So this is not a real issue, and can greatly differ from case to case.
Even the exhausts on the side will find flow restrictions given the high pressures sometimes found on the side skirts, etc. But this is not an easy "science", it has a lot of variables...
On the performance side (aside of the aero point), why short exhausts?
You know, in resume, short pipe means faster travel of the pressure and sound waves (backpressure comes earlier to the valves, etc.). This equals to fast pulsing, which helps at higher revolution ranges. So it's not good for the lower range of revolutions, or for low maximum revolution engines.
In terms of Honda race cars, it could be seen in some early Group A cars in Japan. Then later on the JTC or JTCC series they kept the short design exhausts, but rather than exiting on the side, these had the exit at the underside... nowaydays it's nearly impossible to see some Honda race car with sided exhaust.
Also some old race Toyota had these type of exhausts there in Japan (some N2 series AE86...).
As exhaust science is constantly changing, and they find things they didn't know before...
Keep your exhaust on the long side, to the rear better