Can a lone transport pass through an enemy submarine occupied sea zone with nothing happening or would it be considered a naval attack?
Sea units can safely enter or pass through territories occupied by enemy submarines only
As stated in its profile on page 30 of the rule book, a submarine has the characteristic "Does Not Block Enemy Movement" which in short allows enemy ships to ignore their presence. No combat is triggered if the player entering or passing through the zone does not choose so.
Be aware that this has nothing to do with transports specifically, but is a characteristic of submarines and applies to all sea units.
Full text of the characteristic for reference:
The “stealth” ability of submarines also allows enemy ships to ignore their presence. Any sea zone that contains only enemy submarines does not stop the movement of a sea unit. Sea units ending their combat movement in a sea zone containing only enemy submarines may choose to attack them or not. Sea units can also end their noncombat movement in a sea zone containing only enemy submarines.