I have a 2hp Honda which I have used on both dinks and inflatables. It is a short shaft, and for general use I would not recommend a long shaft. The exception would be if it needed to be used on other boats which could not use the shortie.
In addition to the reasons others have given, my reasons are:
The little Honda is direct drive, which means that if the motor is running the prop is turning. If starting from the beach or rocks that means you must be considerably deeper when starting or stopping the engine.
On a beach or shore with a gentle slope that additional 5" of length can mean many yards of slogging out to achieve enough depth to prevent damage or grounding.
Long shafts work better on short transoms than the other way around, but they still lose efficiency.
The deeper the protrusion below a hull, the more likely to be damaged.
A short shaft when tilted can snake through a surprising amount of seaweed while still steering well. The long shaft not so.
A longer shaft is harder to store.