No a 3 way switch can not be a disconnecting means.
A disconnecting means must have a clearly labeled off or open position.
Depending on your exhaust fan one of these will apply.
Appliances
422.35 Switch and Circuit Breaker to Be Indicating.
Switches and circuit breakers used as disconnecting means shall be of the indicating type.
Motors
430.104 To Be Indicating.
The disconnecting means shall plainly indicate whether it is in the open (off) or closed (on) position.
