I have noticed that the scale difference is quite marked when compared side by side.
An example of this is that I often use the scale 1/48 for my boats. I purchased some figures at a scale of 1/50 and placed them on the boat, next to 1/48 figures. The results were quite obvious.
However, when the 1/50 figures were used in a different location, away from main features, it was not so apparent.
To return to the thread, I should imagine that placing a 1/48 scale boat in your diorama would look quite bulky and out of place.
Another point worth mentioning is, do you intend to cut the bottom part of hull off, so that she appears to sit in water. if so, then this would negate a lot of work in the boat building phase., as you would only need the deck section showing.
I suppose it all comes down to how precise you really want to be.
ken