Thats exactly why I have a 1/4" longer rod in my 427,but again it depends on the application.If it meant running a narrow ring package in a street engine instead of a wider more durable package I would say no.If it meant putting the top ring less then .100" from the top of the piston on just about any engine I would say no.If it meant not being able to get an extra half inch of stroke in the engine I would say no.If it meant going over about 1.85:1 on the rod ratio I would say no unless it was some oddball exmaple of some super short stroke engine that would need 1000 gram pistons just to make it go together,and even then I would be skeptical.
As for induction signals,increasing the speed at which the piston moves away from TDC on the intake stroke causes the demand on the intake to be greater at this part of the cycle,while being weaker at the end of the intake cycle.This isnt good since this requires that the valvetrain be timed to get as much lift at the valve as possible at or around the time the piston crosses TDC to take advantage of the high piston speed,and it means that the slow approach to BDC will somewhat deminish to velocity in the port as the piston crosses BDC and will require an earlier intake closing event which limits RPM potential.This problem was a big issue when Comp eliminator drag engines had to run standard deck height blocks.These engines had a surplus of cylinder head and intake flow,but poor velocity because the ports were typically larger then optimum for these super destroked engines,The problem was made worse by the fact that the only was to get a sane piston weight out of a 3" stroke smallblock with a 9.2" deck height was to run 6" rods which created the induction pulse problems I mentioned above.The problem was further aggitaged be the fact that in order to get more signal up to the carb through the already too big indiuction system,builders took plenum volume out of the intakes which helped low speed signal to the carbs but caused reversion at high speeds.
Think of it like this,a 3" stroke or even 2.75" stroke Comp smallblock could easily run a 6.25" rod in a stock height block with no issues,and a 3.650" stroke 500 cube prostocker could easily run 6.800" rods in a stock height block with no compromise to piston design,but for the same reason
both classes use very expensive and very trick "low deck" blocks that let them use much shorter rods with these combinations.
3 hp per cube normally asperated on gas isnt something to scoff at the last time I checked.