Rather than adding in a giant pile of new ships with every expansion (which will eventually make the game impossibly huge to comprehend)
I don't think it would. Even if there were thousands of ship types, they are all easy to comprehend by reading their descriptions, and you will only ever see 10-20 different types in a single game, depending on how long the game goes on. And since you can easily limit by ship type, you can always pare down the list if it seems like too much to deal with. And I trust that they won't start adding ships pointlessly. We'll never get a ship that's just like a bomber, except its projectiles are a different color. Everything will surely have a niche to fill and be able to distinguish itself in some way.
While it might be comprehensible, having new ships with a nasty ability go unnoticed is still a huge pain. I recently checked for gravity guardians and saw none so I ran some transports through the system, then realised the AI came up with new spire ship that does the same thing and lost about 800 ships.
Actually, is there any chance we could get "priority markers" for ship types? I'm playing 5.000 so zombie and gravity guardians are priority 1 targets as various types of guard posts would be, but it would also let you easily tell when a new type of ship shows up, without trawling through all the stats of everything in the system. An additional display such as highlighting priority 9s would be nice too, but not essential.
EDIT: To be clear I don't mean your ships would actually target it with higher priority - just like setting system priorities it would help you keep track of what you consider important/unimportant.