Do the screws normally penetrate the underside of the deck?
It's not uncommon for them to do so. It will all depend upon the thickness of the subdeck, which is usually a fiberglass-plywood-fiberglass sandwich, the thickness of the teak planking, the length of the deck screws, and depth to which they were countersunk in the planks.
If you find that the deck screws are coming through the underside of the deck when you inspect the inside of the boat it is not reason to think there is something wrong, it's just the way the boat was built.
The bad thing about this kind of deck construction is that the manufacturer builds a boat with a nice, totally waterproof deck and then drills 10,000 holes in it for the deck screws. The screws will invariably penetrate the wood subdeck core and therein lies the potential problem.
If moisture can get under the teak planks, depending on how well they were bedded to the subdeck it's very likely the moisture can then find its way down along the deck screws into the wood core. And we all know what moisture can do to wood over time.
This is why it is so important with a wood-decked boat to keep moisture from getting down under the planks. The two things that do this are the seam sealant and the plugs over the tops of the deck screws. Keep those in perfect shape along with other deck-penetrating hardware like handrail stanchion fasteners, cleat fasteners, etc. and you'll keep moisture from getting under the planks.
Starting in the late 1990s or thereabouts higher end boats like Grand Banks, Fleming, etc. began gluing their teak deck planking to the subdeck rather than screwing it down. This became possible with the advent of adhesives capable of doing this job and it solves the problem of moisture migrating into the wood subdeck core down past a myriad of deck screws.
Unfortunately the ability to do this effectively didn't exist back when so many of the kinds of boats we buy used today were made.