Oldjeep,
I have seen many YJ's and TJ's crossing deep rivers and not die... So I know they can make deep crossings. Of course, after those trips, you will ussually need to change out all the fluids, and that is logical and understandable, but just because the water is deep does not mean the engine compartment is completely flooded because there is always a bubble in the engine compartment.
Now, I agree with you that a snorkel does not make an engine submersible, and that besides what you mentioned, other things can be totaled (like the computer for one!), but my point is that a snorkel does make deeper water fording possible (although not necessarily advisable).
For example, this Jeep crossed a river I would not dare to cross without a snorkel (this one belongs to a friend, and it is a 4.0L crossing in 2H). This crossing was made twice in that day (going and coming back), and no mechanical damage was done to the engine (mind you all fluids were changed afterwards). I DO have to admit the the computer died about a week later (going back to my comment about a snorkel not making a Jeep waterproof!), but it was the only jeep to suffer any problems (many others crossed as well).
Felipe