Good concepts in general. To be picky, though, in practice neither the ship limit nor the lack of real-time movement are actual reasons for small ships' inefficiency in SE4.
The limit of 20,000 ships per nation is rarely, if ever, reached, and it'd be even more unlikely to become a factor. That only matters in games where players chose a low limit on the number of ships (or perhaps a really enormous game).
The lack of advantages for smaller ships is an issue with the game settings. Mods such as Proportions demonstrate that SE4 can be set to represent advantages of smaller ships. And a real-time game can still easily not include appropriate advantages of small ships in the settings. StarFury gives some advantages to smaller ships (mainly, better turning rates), but still is simplified in several ways that give larger ships advantages that don't seem to have a basis in logic. Fortunately, both games are moddable.
PvK