They are very nice indeed, though - besides the fact that these funnels indeed look bit odd (but I understand Your rationale), I have some doubts about height of the decks on some ships (judging by the space between windows or by the construction elements).
For example Ceasar-class cruiser has a lookout on the main mast, which is 11 pixels high
from the bottom side of the floor to the top of the roof - and 11 pixels is 165 centimeters or 65 inches - from which You have to subtract thickness of the floor and roof (3 pixels each, by SB standards - but let's just count it as 4 pixels - 3 for floor, 1 for roof - it leaves 7 pixels to move inside - 107 centimeters, or 42 inches).
And basically all Your ships have similar issues.
But other than that, it's a nice start!