All I can say is ouch. We loaded up our game with just 9 AI planets left and the threat went from 400 something to 13,940. The entire game ran rather sluggish compared to previous weeks thanks to the sudden consumption of system resources brought about by the 13,500 ships that had previously not been a CPU burden thanks to cold storage. I might say this area may need some more balance, particularly if those ships remain behind enemy lines doing nothing observable (i.e., wasting CPU time), but this is an old game and this is likely an artifact not specifically of the high AI progress (2400) but rather the high numbers of AI ships (one AI is a turtle, if I recall) on each of the remaining planets. There are roughly 50,000 AI ships left and only 9 planets for them.
Since cold storage was introduced to improve performance, this mechanic may need some tweaking, because as it stands cold storage is going to be far less effective at reducing CPU load during high AI ship count games.
Yeah, I was thinking about you with this -- I mean, with really old games like that, this would break them. This normally would not be a performance drain, because those ships won't stay behind enemy lines -- all 14,000 of them should be attacking you imminently. Normally if you were playing an entire game with this mechanic present, the ships would never build up to quite that degree, and you'd be facing more attacks all throughout, and the entire mechanic is a bit different. I think you'd still be able to play your sort of game, and without any particular performance penalty (if anything, this will help even more than cold storage as far as CPU savings go, because it keeps the total number of AI ships a bit lower over time), but with certain unusual older games like yours, it may be a rough transition to be sure.
I am not surprised that the game ran more sluggishly there, but I am surprised that these guys weren't attacking you; that is really odd.