The transport balance is something we have been keeping an eye on, and adjusting in the betas so far.
If you play long enough, any AI planet will "fill up" to whatever its max number of ships are based on guard posts, etc. But when that happens, typically the galaxy-wide ship count is north of 70,000 units, so the AI starts combining its ships. Two Mark I ships equals 1 Mark II ship, and so forth. That logic is actually a short term loss for the AI, but it lets them consolidate and then do more reinforcements, so planets keep getting more difficult as the game progresses, even after all the planets have all hit their cap -- they are simply "teching up" instead of getting larger in numbers.
If you were to play a single campaign long enough (at least 30-40 hours, it seems, from player reports), you eventually end up with all AI planets being fully capped out with Mark V ships. This is not really a worry unless you are playing a super completionist game. If you are to that point, you also have the resources and such to deal with it. That's what keeps the game interesting and from just hitting an "end state" for the AI at any point remotely near the length of most player campaigns (sub 20 hours).