How long to sharpen Japanese knife with whetstone
The answer partly depends on how dull the knife is when you go to sharpen it.
Most electric knife sharpeners have 2 or 3 different wheels with coarser and finer grinders, the coarser allow you to establish the angle of the edge and the finer grain refine it, similar to coarser and finer sandpaper.
The two disadvantages of sharpening with a whetstone are that you generally only have one grit or fineness to use (though some whetstone kits have more), and if you are freehanding the sharpening, it may be difficult to hold the right angle if you are sharpening for a long time.
So if you are starting with a very dull knife where the angles of the edge are off or if there is damage, it might take a lot of sharpening to establish them, and unless you're holding the stone at exactly the right angle all the time, you might not end up with a good edge.
On the other hand if the blade already had a good edge and you sharpen it frequently with a whetstone, like every few uses, then you are just fine tuning the edge and this should be fairly quick.  I would say somewhere between 10 and 50 strokes depending.