hull upgrades can go both ways. USAF operates airframes that are over 50 years old (transports and tankers). but the f-111 vs the f-117 is a definite hull upgrade due to new materials. note that both are deep penetration ground strike aircraft. one pre-stealth, and the other post-stealth. this is somewhat similar to the tiger I vs tiger II, where the hull itself was one of the the major new technologies in the design. the t-34 is another example of a "new kind of hull" type design.
the US navy commonly will rip out the entire guts of a ship to refit it over course of many months. about the only thing they can't do is put intercontinental ballistic missiles on a ship not originally deigned for it, and they can probably do that too, given enough time.
there's no reason to think that such behavior patterns would not occur in the future, any future, unless you have game universe rules that make it otherwise.
so you probably only need hull upgrades when you have changes in hull technology - which would most likely be the result of completing a node on the research tree.
by limiting or eliminating changes in hull technology you can limit or eliminate hull upgrades.