The jets
will ingest a lot of oyster shells and other debris. The jet boat could
probably plow right through an oyster bar and keep right on operating

Gee, destroying the waters they're trying to research isn't exactly sound
logic. I'd also wonder how much more damage the water flow from the jets
would cause during maneuvering a boat of that size.

Not saying this as an argument for props though. More that it's dumb to
plan to go into places that will very likely cause greater harm to the
enivonment that necessary. Take a dinghy or launch instead, not some huge
vessel.