I have avoided this--we have discussed it before. But here goes. Flint (chert) can have micro porosity and can have water in it. The question is whether or not it will absorb water in a jar etc. and whether or not that "helps" the flint in use. As for water bound in the "lattice" someone mentioned--yeah you can probably drive some off with heat, but taking it back in through sitting in water is a different matter. Chert [flint] formed originally in a water-rich environment and water can be taken up within its structure. Some chert containd amorphous opalline SiO2 which can contain water too. But in general the quality flints used for knapping have no [or very microscopic] pores. Do you remember surface tension from your HS physics? Capillary pressure? stuff like like? The tiny pores may not allow water passage. Cherts can be aquifers (water carriers) in nature, where in situ they are bedded rocks--via fracture networks in the rocks much more so than pores (which can exist). The famous Hot Springs of Arkansas are thought to be related to fractured chert aquifers. Heard of Washita stones and Hard Arkansas stones? Both chert [novaculite]and identical in composition, but the Washita stone has a little porosity, which gives it a more "granular" feel, thus it cuts steel better than the "Hard" variety, which has the same hardness, but is "smoother" (essentially no porosity) and polishes the steel [think in terms of coarse versus fine sandpaper for the effect, although cause is different]. Flint put in water, if fractured or porous, could take up a little water--but I see no advantage to that, in fact it might mask weaknesses in the flint. The best flint for knapping has no fractures or significant porosity. Chert [flint] is micro- to crypto-crystalline silica. Sometimes it contains opal (noncrystalline silica), water and impurities (calcite, fossils, silt, clay, organics, etc). This means that pores [spaces between the microcrystals] are very tiny IF THEY EXIST. Typically the pores are full of natural cements such as more silica or calcite. Sometimes the calcite can be dissolved out "restoring" the porosity. But in general I think you can safely ignore the water soaking....
P.S. I left out the permeability factor--chert [flint] is typically impermeable, which means water wont' penetrate very far into it, even if the pores are present.