Chuck,
Okay then why the concern over rotted wood in the stringer?

Depends on the stringer. Did the manufacturer intend to have an FRP stringer
that just happens to to have a wood or foam core, or did the mfg put 3/32 inch
of glass to "encapsulate" a wooden stringer where the wood was actually bearing
the stress?

I would
imagine that the water got in through a poor job of sealing the wooden
stringer, so why not seal it up and not worry about it?

See above. I've attended surveys where a decayed stringer core has been
detected, and in some cases the stringer is condemned as a result and in others
it is not.

I know a fellow that had his boat (88 Sea Ray 300
Weekender) out of the water for three seasons while he dried out his
stringers and checked for moisture with a meter.

Hooooo, boy. Find out whatever it is that guy wants to buy and go into the
business of selling it to him.

You can't "dry out" decay.

Each case is different, but a stringer repair should be doable in a matter of
days, not years. I'm aware of situations where the stringer has been sliced
open, the old core excavated, new core material substituted, and the whole
works glassed back up. Another cure that surveyors have signed off on, (again,
depends on the stringer), involves building up the laminate to increase the
load bearing ability of the stringer perimeter.

I think he then bored some
holes in the stringer and filled with epoxy. Was he wasting his time?

Three years to do a cheap and dirty Git-Rot fix? Yeah, he was wasting his time.
:-)

His
complaint was that Sea Ray drilled limber holes through the stringers and
didn't seal the limber holes causing the water absorption. I'm just trying
to determine how wide and important of a problem is this.
Paul

Unsealed limber holes are fairly common in production boats. :-(

It is a bit griping how so many builders, (not just a few) turn out a product
that will maintain fair to good structural integrity for
12-15 years, and then price it at $250k or up- and the typical buyer needs a
20-year mortgage to pay for it.