quite simply, transports have to be defended, and the allies can put have in range alot of threatening airpower before japan’s second turn… and every ship that’s left defending them reduces your ability to cheaply destroy the various allied fleets that might be making a mess in the pacific on turn one.
Other than that, the additional transports allow for 6 units a turn, similarly to the IC’s. The additional transports give you the ability to grab guys more quickly from the islands, as well as the ability to push on india and africa faster and harder. But each of these require some tradeoffs (ideally, mass troops in manchuria, but if india looms you may have to deal with that, slowing the flow of 6 units/per turn.
transports assuming a factory build later also ends up reducing the flow of fast moving armor, if that’s necessary.
Don’t get me wrong, i’m a big fan of transports, but they have their drawbacks too.