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You can resize them, in interface folder there is mapitems.gfx

In the part
meshType = {
name = "harbour"
xfile = "gfx\\mapitems\harbour.x"
effectFile = "gfx\\FX\mapobject.fx"
scale = 2
}
meshType = {
name = "harbour_ships"
xfile = "gfx\\mapitems\harbour_ships.x"
effectFile = "gfx\\FX\mapobject.fx"
scale = 2
}
You can put scale = 1 to make their size half, I didn't test for smaller scales (<1).