Yes. Air units can attack Naval units (except for Submarines unless the air unit(s) are accompanied by a destroyer), and so they automatically sink undefended transports.
The other idea is that no one can be in Russian territory except Axis and Russians which also significantly increases Germany’s odds and again, encourages Japan to attack America since America really has nothing better to do than help in Africa and attack Japan.
If the defender has transports they cant be allocated as hits in any combat round. They are invisible and automatically removed from play provided the non-transports have been removed as combat loses. If the attacker does not stay long enough to kill the last combat ship the defending transports remain in place.