The real answer to your question might actually hinge on your personal definition of "significantly reduced vertical seperation [sic]", as much as on the TYPE of approach being used.
If the aircraft is conducting a visual approach, then the old saying "a miss is as good as a mile" might apply. If the aircraft is executing an ILS approach, the protection area for the precision segment will take account of the Obstacle Limitation Surfaces that are established for approach and landing (plus overshoot), together with a complex algorithm that considers all types of obstacles in the Collison Risk Model. This is the most likely situation for your scenario because the actual clearance over any obstacle will be much less than for a non-precision approach.
And now to the non-precision approach situation. Ships are most certainly regarded as obstacles and a general allowance of 200 feet is made for the height of a ship. Obviously, if taller ships are known to frequent the area, this minimum height allowance needs to be increased accordingly. On top of this, the minimum obstacle clearance in the final segment can be as little as 246 feet (Pans Ops criteria).
That's not a lot and it can indeed look like a lot less, depending on your position when making the visual observation. The fact is that, unless you have a really good eye for judging altitude, a clearance of just 246 feet can seem like very minimal clearance. And, unless you are exactly at a right angle to the line of flight at the time the aircraft crosses over a ship, you will have a paralax error that will make the height clearance seem like next to nothing.