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.
When done correctly, using correct pocket depth and properly size PH fastener, (along with some gorilla glue} this is not a issue
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.
again, not really an issue, but I would use the pocket plug anyhow, you can get them in most all species
Pockets are fine for tables, interior furnishings and any non-critical assemblies. But for anything else the potential risks are too high.
I was thinking this is what deniseO30 was talking about
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.
the time envolved using a PH jig is minute and the advantage over glue and ringshank is enormous, a nail, any nail work by forcing aside material and relying on friction as material compresses back around the nail to hold.
A pocket hole, you're using a stepped bit that creates not only the pocket but also a shoulder, then continues with a pilot hole into the joining material, the pilot hole is smaller dia than the PH screw which is self drilling and only threaded about a 3rd of the screw shank, the remaining shank is smooth.
If done correctly you end up with a clamping force between the screw head sitting on the shouldered pocket and the screw thread that has pass completely though the pocketed stock into the joining material.
This in addition to a good wood binder is very strong