A little run down from a geo/petrological perspective...
The big no-no when soaking natural stones is trying to do it on stones that are fissile or display noticeable cleavage. The kind of stone that will break into sheets along straight lines, and is a feature mostly associated with metamorphic rocks, like slates. It's a product of lithification (pressure), and heat.
Most jnats are wholly or predominantly sedimentary rather than metamorphic. They can still sometimes be fissile as a result of lithification (like shales) but don't display quite the level of cleavage that slate does. When you see layers in the sides of suita for instance; that isn't fissility, it's the bedding planes of the initial deposits.
Different bedding planes are not an inherently different part of the structure of a stone in the same way that different layers of cleavage are. However they are still different stuff from each other, and different stuff has different properties, porosity, and absorption. This is why you still want to be sealing the sides of jnats, but sealing the bottom doesn't matter at all, and in fact I think could possibly be detrimental on some stones.
In general Japanese stones are going to be more accommodating when it comes to soaking than the majority of historic European honestones, which were very often slates, but there is still obviously a risk.
Jnat soaking guidelines: Don't soak stones that look particularly heterogenous or layered from the side. Don't soak stones with suji or su. Don't soak stones with hairline surface inclusions. Don't soak very heavy stones. Don't soak very fine stones.