As a '97 GS owner myself, I can offer the following observations:

The factory electric moonroof has drain tubes to carry the water away.  
The moveable part doesn't really 'seal' to the metal roof, rather the
water simply seeps around the edges into the channel that surrounds it,
then down the drain tubes.  If the roof is aftermarket, however, you
have a very different situation where the removeable glass panel must
seal via gasket to the metal roof.  In my area, factory moonroofs are
not so common on RS models and fairly standard on GS models. If it's
electric, it's factory - if removeable, it's aftermarket.

The passenger airbag cover being raised is common, particularly around
the edges.  I think this is in part due to summer dashboard heat causing
the adhesive on the padding to fail.  Also, even a perfect one will seem
to be slightly raised (not flush).

The air intake, probably with a K&N filter, is controversial, and at the
risk of starting a long heated thread, I have to say I don't care for it
myself.  But all you need to do is Google K&N and you'll find arguments
on both sides of the fence.  My rationale - I know of several 420A
engines running the stock setup that have nearly 200K miles and still
deliver nearly 32-34mpg on the highway.  A salvage yard could probably
provide the stock arrangement for little money.

$2800 seems like a fair price for a clean example.  If it hasn't had the
timing belt replaced, or if you can't determine that, I'd do it right
away.  Do the water pump while you're in there.  You might also want to
put the car on a lift and check the back of the engine for oil seepage
around the head gasket.  I had to replace my head gasket at around 100K,
and it seems like it was around $600 to do all of the above.

Geary

I do enjoy my 97 GSX but generally reserve the recomendation of this vehicle
to someone who is intent on modding the car for sport or racing.
The Eclipse is pretty but is worse than average in terms of reliability.
You can pick up an OE intake on Ebay or in the classifieds at
www.dsmtalk.com or www.dsmtuners.com
The K&N is a good filter but the "cold air" versions that are routed low do
represent a hydro-lock hazard as you have suspected. On the turbo equipped
cars, the K&N is good for 15 hp on an otherwise stock car. The OE intake is
really restrictive. What most folks don't realize is that stock intakes are
designed as much for noise reduction as they are for engine performance and
therfore are very compromised .
The motor in this model, 420A, is one that's been supplied by Chrysler and
is common to the Neon.

Take into consideration these two facts.  One, the previous owner
could not afford to have the roof fixed properly, and Two,
modified the engine in an attempt to get more power.

This would tell me that the car has been driven hard and
maintained poorly.  I wouldn't touch it with a stick.