In addition to the potential rot paulk mentions, the pockets remove material and create weak areas in the wood.
Most broken items I've seen that were built with pocket screws, have failures where the pockets were.
Filling the pocket with tight fitting glued in dowels -may- approach the strength of the original material, but I wouldn't want to rely on it.
Pockets are fine for tables, interior furnishings and any non-critical assemblies. But for anything else the potential risks are too high.
When you consider the added time required to use pocket screws, there is no advantage. Glue or ring shank nails will have far more holding power.