I'm not sure I understand what is leaking? Water out of the Vdrive unit? Water out of the hull at the prop shaft? Oil out of the Vdrive?
It sounds to me like water leaking out of the hull, so my first recommendation (if you trailer your boat) is always take the plug out. Your boat can fill up with rainwater like an old hottub over a winter, and that literally will total it. The water has to get at least about a foot deep before it reaches any electrical items, though.
Pooled water around a shaft seal that freezes will not damage anything. It has to be trapped in a fixed volume (like the motor) to do damage. Do you know if you have a standard rope packing seal, or a zero leak seal? Either type could be just leaking. Rope seals can be adjusted, but it's probably the most difficult regular maintenance item to perform on a Vdrive.
The hole in your cover is probably a vent, and is a good thing to have. It allows moisture trapped under the cover to escape, for reduced mold growth. Boats can sit out in the rain with no cover on just fine - water leaking in should not be a problem.
Water leaking out of the motor or Vdrive is a big problem, but you said it's been winterized... It has to be in the 20's for 8+ hours before you have anything to worry about.