Because a destroyer is cheaper.
You cannot buy 2 transports and a carrier on Japan 1. That means trading in a transport to get a carrier, not a trade I want, or getting two transports (3 or 4 total available on Japan 2) and a destroyer thus not tying up your fleet on such non-sense as transport protection duty.
Not to mention, when I go after the American fleet with Japan, I always wish I had another destroyer. I never wish I had another transport. (Talking rounds 12+ when Japan goes after the Allied fleet to protect S. Germany)