The problem with very short stroke engines is the lack of leverage on the crank.
For a given capacity, a short stroke engine will have a bigger bore & therefore more piston area. This means that for a similar cylinder pressure (measured as BMEP) the force acting on the piston will be proportionally greater. More force, shorter lever = similar torque.
If you do the calculations for a wide range of bore/stroke ratios you'll find that, for a given cylinder capacity & BMEP the torque varies only by a tiny percentage.
It's interesting to compare real-world examples. Going back to the 1960s, the Ford Anglia had very oversquare engines, while the BMC A-series was a relatively long-stroked 'slogger'. In reality, the 1098cc engine in the Morris Minor 1000, 64.6mm bore, 83.7mm stroke, made 48 bhp @ 5,100 rev/min, 60 lb ft torque @ 2,500 rev/min, while the 1,198cc version of the Kent engine, 80.96mm bore, 58.17mm stroke, made 48,5 bhp @ 4,800 rev/min, 63 lb ft stroke @ 2,700 rev/min.