What happens if I play Stupefy on my 1 [M] empowered Gangplank, Naval? Will he get +3 [M] this turn?

He will not.

In order for his replacement effect to apply, the event of him being given -[M] must occur. In the case of Stupefy played on a 1 [M] unit, no -[M] is given; it is snapshot to -0 [M]. Thus, there is no suitable event for Gangplank’s replacement effect to replace.