Looking at various comparative silhouettes for the Enterprise family of starships, I am struck by how nacelle sizes are relatively constant in width and tend to get somewhat proportionally longer. This is not based on any science fiction physics of warp drive but an aesthetic that fans and designers alike have settled on as an informal consensus. The Sovereign nacelles are among the largest (I don’t have an Odyssey comparison pic handy right now) but only in terms of length – the galaxy and the Ambassador’s nacelles are much wider. Some of that may be to tech improvements but the general aesthetic I am seeing is that – again, not based on warp physics speculation – the nacelle width and length looks most pleasing when they are reflective of the ship dimensions overall.
That said, there does seem to be an upper limit. The Enterprise-J, which is really a portable biosphere, breaks all of these assumptions. However, if you truly had a massive station-sized ship – eg Starbase 1 or Spacedock – would you just attach mega nacelles to it? Defiant shows us that external nacelles aren’t even necessary. Suppose you wanted to build a giant colonizing ship (like the Enterprise-J, which is technically an alternate timeline and not canon), or a mobile spacedock (something along the size of the ships in Banks’ Culture series). I think nacelles wouldn’t even be necessary above a certain size. But if you wanted to have nacelles, perhaps arrays of nacelles would be better – a port array of four, a starboard array of four, a ventral array, etc. These could be Sovereign-style nacelles rather than Stargazer-size.
Above a certain size, even the assumptions of a primary hull, secondary hull, etc break down. My theory is that at some point it just becomes more effective to approach a sphere or a cylinder in shape as ship size scales up. The biggest Starfleet space vessel we have seen is the new Spacedock which is already mostly cylindrical. And Borg ships tend towards simple geometries as well with no need for nacelles. These shapes are probably more efficient in a (fictional) warp physics sense than the elongated saucers of starships and therefore don’t need nacelles per se.