All in all, I think that neutral buoyancy should be kept in the game, because you can rely on your crew to correct the depth with ballast tanks... "Negative buoyancy global behaviour" (and not the "effect" which really existed) is probably more unrealistic than the "neutral buoyancy behaviour" of the original SH3 game. As we say : the road to hell is paved with good intentions.
And, most of all, I think we should once and for all forget the idea of getting something close to the reality with this old and defective game... (I particulary think about this dumb, ultra basic and surrealist so called "artificial intelligence"... (we should call it "pre-programmed behavior")).
Sorry for being pessimistic, but this is my conclusion after years of playing and modding this game, and reading testimonies and history books on the (anti-)submarine warfare... Improvements are only possible at the margin and do not change much. Of course, I will never blame the work of modders who invest (many) hours of their free time. It sure adds some nice touch to the game (that we call "eye candy"). But again, after some time, one always realizes that this is mostly "cosmetic"...
I wish you all the best. After all, this game is just... a game... which has only a distant connection with historical reality (facts)... Games are designed to be funny and entertaining, not to be real simulations. War is boring, sad and horrible. It's a personal experience of the worst that humans can do. A "game" will never truly simulate a war (else, everyone, except psychopaths, would become pacifists... which would be a good thing IMO).