A kamikaze strike can target any specific
enemy surface warship (not a submarine or transport)
belonging to the attacking power.
Page 16 of Pacific 1940 2nd Edition rulebook.
If you have a transport alone next to an island with an airbase and fighters, can an enemy sub get “free” kill on that transport?
Yeah. The fighters can scramble to defend, but without a destroyer present they can’t target the sub.