I would think short shaft is always OK for an inflatable. Long shaft is for bigger boats who have the engine mount too high to guarantee keeping the prop below water at all (most) times.
Measure from the top of the transom of your boat to the bottom of the keel immediately below the centre of where you are going to place the o/b.
Approx 16", short or standard shaft.
Approx 20" long shaft.
Most inflatables are short shaft, but CHECK first. A short shaft will not work properly at all if the prop is spinning behind or too close to the bottom of the transom. There may also be cooling restrictions.
Using a long shaft when you should be using a short shaft is dangerous as the extended drive point below the transom can cause the bow to ride up or even flip.
Assuming a 2 to 3.5 hp outboard on a small inflatable here - short shaft is usual.
Main problem with a longshaft outboard on a small inflatable is likely to be poorer starting: the exhaust being immersed too deeply causing back pressure. Once it does start a longshaft will be fine, not enough power in small outboards to cause much trim problems. I've used longshaft o/bs on small dinghies often enough (to use the same engine to power small yacht and its tender).